Evolution of TALENs

ABSTRACT

Engineered transcriptional activator-like effectors (TALEs) are versatile tools for genome manipulation with applications in research and clinical contexts. One current drawback of TALEs is that the 5′ nucleotide of the target is specific for thymine (T). TALE domains with alternative 5′ nucleotide specificities could expand the scope of DNA target sequences that can be bound by TALEs. Another drawback of TALEs is their tendency to bind and cleave off-target sequence, which hampers their clinical application and renders applications requiring high-fidelity binding unfeasible. This disclosure provides methods and strategies for the continuous evolution of proteins comprising DNA-binding domains, e.g., TALE domains. In some aspects, this disclosure provides methods and strategies for evolving such proteins under positive selection for a desired DNA-binding activity and/or under negative selection against one or more undesired (e.g., off-target) DNA-binding activities. Some aspects of this disclosure provide engineered TALE domains and TALEs comprising such engineered domains, e.g., TALE nucleases (TALENs), TALE transcriptional activators, TALE transcriptional repressors, and TALE epigenetic modification enzymes, with altered 5′ nucleotide specificities of target sequences. Engineered TALEs that target ATM with greater specificity are also provided.

RELATED APPLICATIONS

This application is a continuation of and claims priority under 35U.S.C. § 120 to U.S. patent application U.S. Ser. No. 15/748,053, filedJan. 26, 2018, which is a national stage filing under 35 U.S.C. § 371 ofinternational PCT application, PCT/US2016/044546, filed Jul. 28, 2016,which claims priority under 35 U.S.C. § 119(e) to U.S. ProvisionalApplication, U.S. Ser. No. 62/198,906, filed on Jul. 30, 2015, which isincorporated herein by reference.

GOVERNMENT SUPPORT

This invention was made with government support under HR0011-11-2-0003awarded by the Department of Defense. The government has certain rightsin the invention.

BACKGROUND

Genome-editing tools have the potential to revolutionize ourunderstanding of how genotype influences phenotype, facilitate thedevelopment of organisms of industrial and biomedical relevance, andserve as treatments for genetic diseases^(1,2). These tools includemeganucleases^(3,4), site-specific recombinases, RNA-guided nucleasessuch as Cas9⁶, and fusions of programmable DNA-binding domains (DBDs)such as zinc fingers to effector domains including nucleases,recombinases, and transposases^(4,7). Zinc fingers (ZFs) are naturallyoccurring DBDs of approximately 30 amino acids that typically bind threebases of DNA along the major groove⁷⁻⁹. Several methods have beendeveloped to generate zinc-finger arrays with tailor-made DNAspecificities^(10-12.)

Transcription activator-like effectors (TALEs), have emerged asattractive alternatives to zinc fingers for sequence-specific DNAtargeting⁷. TALEs consist of an N-terminal domain followed by a seriesof tandem repeats each of 33 to 35 amino acids, a nuclear localizationsequence, a transcription activation domain, and a C-terminaldomain^(13,14). Two repeat variable diresidues (RVDs), typically atpositions 12 and 13 within each repeat, recognize and bind to a specificDNA base^(15,16). Altering the RVDs allows TALE repeats to be programmedusing a simple code^(13, 17). Unlike ZFs, TALE arrays are thought tobind DNA in a fairly context-independent manner facilitating the designand assembly of arrays to target long sequences^(7,18,19). TALEs havebeen fused to various effector domains to generate site-specificDNA-cleaving enzymes (TALENs)^(7,20,21) epigenome-modification enzymes,and transcriptional activators and repressors^(14,17, 24,25).

SUMMARY OF THE INVENTION

One limitation of TALEs is that the 5′ nucleotide of the target sequenceis specified to be T^(15,26,27). TALE domains with alternative 5′nucleotide specificities could expand the scope of DNA target sequencesthat can be bound by TALEs. Although promiscuous TALEs with nospecificity at the 5′ position have been described^(28,29), no TALEvariants that preferentially recognize 5′ A or 5′ C have been reported.In addition, the DNA sequence specificity of DBDs is a crucialdeterminant of their safety and usefulness as research tools and humantherapeutics. While TALEN architectures were previously engineered withimproved general DNA-cleaving specificity by reducing excessnon-specific DNA-binding³⁰, enhancing the specificity of a particularTALE array in a targeted manner by decreasing its ability to bind tospecific off-target DNA sequences found in a genome has not beenaccomplished.

Some aspects of the instant disclosure are based, at least in part, onthe surprising discovery that TALE mutants that preferentially bind anon-canonical 5′ nucleotide (A, C, or G) over the native 5′ T can beevolved using phage-assisted continuous evolution (PACE), therebyexpanding the scope of DNA target sequences that can be bound by TALEs.Modified TALE proteins that bind a target site with a non-canonical 5′adenine (A), cytosine (C) or guanine (G) and methods of using suchmodified TALE proteins are described herein.

Some aspects of the instant disclosure are based, at least in part, onthe surprising discovery that PACE can be used to increase thespecificity of an ATM-targeting TALE to its target site relative toknown off-target sites. Accordingly, described herein are modifiedATM-targeting TALE proteins that preferentially bind to an ATM targetsite relative to an off-target site and methods of using suchATM-targeting TALE proteins.

Some aspects of this disclosure provide modified TALE domains.

For example, some aspects of this disclosure provide proteins comprisingan amino acid sequence that is at least 80% identical to the amino acidsequence provided in SEQ ID NO: 1, wherein the amino acid sequencecomprises an alanine to glutamic acid amino acid substitution at aminoacid residue 39 (A39E) of SEQ ID NO: 1 or a homologous residue in acanonical N-terminal TALE domain, and/or a lysine to glutamic acidsubstitution at amino acid residue 19 (K19E) of SEQ ID NO: 1 or ahomologous residue in a canonical N-terminal TALE domain.

Some aspects of this disclosure provide proteins comprising an aminoacid sequence that is at least 80% identical to the amino acid sequenceLTPX₁QVVAIAX₂X₃X₄GGX₅X₆ALETVQRLLPVLCQX₇HG (SEQ ID NO: 2), wherein X₁ isD, E or A, wherein X₂ is S or N, wherein X₃ is N or H, wherein X₄ is G,D, I, or N, wherein X₅ is K or R, wherein X₆ is Q or P, wherein X₇ is Dor A, and wherein the amino acid sequence comprises one or more aminoacid substitutions selected from the group consisting of T2A, P3L, P3S,X₁4G, X₁4K, X₁4N, X₂11K, X₂11Y, X₃12H, X₄13K, X₄13H, G15S, X₅16R, X₆17P,T21A, L26F, P27S, V28G, Q31K, X₇32S, D32E, and H33L.

Some aspects of this disclosure provide proteins comprising an aminoacid sequence that is at least 80% identical to the amino acid sequenceprovided in SEQ ID NO: 3, 4, or 5, wherein the amino acid sequencecomprises a glutamine to proline amino acid substitution at amino acidresidue 5 (Q5P) as compared to either SEQ ID NO: 3, 4, or 5, or ahomologous residue in a canonical C-terminal TALE domain.

Some aspects of this disclosure provide proteins comprising thestructure [N-terminal domain]-[TALE repeat array]-[C-terminal domain];wherein the N-terminal domain comprises an N-terminal domain providedherein, the TALE repeat array comprises a TALE repeat array providedherein, and/or the C-terminal domain comprises a C-terminal domainprovided herein.

Some aspects of this disclosure provide proteins comprising an aminoacid sequence that is at least 80% identical to the amino acid sequenceprovided in SEQ ID NO: 12, wherein the amino acid sequence comprises oneor more amino acid substitutions selected from the group consisting ofA76T, K84R, D134E, L162S, A222S, K288R, Q329K, R330K, A338T, A392V,A416V, P435Q, V464I, L468F, and K512R.

Some aspects of this disclosure provide proteins comprising an aminoacid sequence that is at least 80% identical to the amino acid sequenceprovided in SEQ ID NO: 1, wherein the amino acid sequence comprises oneor more amino acid substitutions selected from the group consisting ofQ13R, A25E, W126C, and G132R, or a homologous residue in a canonicalN-terminal TALE domain.

Some aspects of this disclosure provide proteins comprising an aminoacid sequence that is at least 80% identical to the amino acid sequenceprovided in SEQ ID NO: 13, wherein the amino acid sequence comprisesamino acid substitutions (a) Q53R and A252T; (b) W166C, K260R, A398S,A514T, A592V, and Q745P; (c) A252T, Q505K, and Q745P; or (d) A252T,L338S, Q505K, and Q745P.

Some aspects of this disclosure provide methods comprising contacting anucleic acid molecule comprising a target sequence with (a) a proteincomprising a modified TALE domain, a modified TALE repeat array, or amodified TALE protein as provided herein.

Some aspects of this disclosure provide methods of phage-assisted,continuous evolution of a DNA binding domain, wherein the methodscomprise (a) contacting a flow of host cells through a lagoon with aselection phage comprising a nucleic acid sequence encoding aDNA-binding domain to be evolved, and (b) incubating the selection phageor phagemid in the flow of host cells under conditions suitable for theselection phage to replicate and propagate within the flow of hostcells, and for the nucleic acid sequence encoding the DNA-binding domainto be evolved to mutate; wherein the host cells are introduced throughthe lagoon at a flow rate that is faster than the replication rate ofthe host cells and slower than the replication rate of the phage,thereby permitting replication and propagation of the selection phage inthe lagoon; and wherein the flow of host cells comprises a plurality ofhost cells harboring a positive selection construct comprising a nucleicacid sequence encoding a gene product essential for the generation ofinfectious phage particles, wherein the gene product essential for thegeneration of infectious phage particles is expressed in response to adesired DNA-binding activity of the DNA-binding domain to be evolved oran evolution product thereof, wherein the selection phage does notcomprise a nucleic acid sequence encoding the gene product essential forthe generation of infectious phage particles; and wherein the flow ofhost cells comprises a plurality of host cells harboring a negativeselection construct comprising a nucleic acid sequence encoding adominant negative gene product that decreases or abolishes theproduction of infectious phage particles, wherein the dominant negativegene product is expressed in response to an undesired activity of theDNA-binding domain to be evolved or an evolution product thereof.

Some aspects of this disclosure provide methods of improving thespecificity of a DNA-binding domain by phage-assisted, continuousevolution, wherein the methods comprise (a) contacting a flow of hostcells through a lagoon with a selection phage comprising a nucleic acidsequence encoding a DNA-binding domain to be evolved, and (b) incubatingthe selection phage or phagemid in the flow of host cells underconditions suitable for the selection phage to replicate and propagatewithin the flow of host cells, and for the nucleic acid sequenceencoding the DNA-binding domain to be evolved to mutate; wherein thehost cells are introduced through the lagoon at a flow rate that isfaster than the replication rate of the host cells and slower than thereplication rate of the phage, thereby permitting replication andpropagation of the selection phage in the lagoon; and wherein the flowof host cells comprises a plurality of host cells harboring a negativeselection construct comprising a nucleic acid sequence encoding adominant negative gene product that decreases or abolishes theproduction of infectious phage particles, wherein the dominant negativegene product is expressed in response to an undesired activity of theDNA-binding domain to be evolved or an evolution product thereof.

The details of one or more embodiments of the present disclosure are setforth in the accompanying Figures. Other features, objects, andadvantages of the disclosure will be apparent from the DetailedDescription, the Examples, and from the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1D show the development of a DNA-binding continuous evolutionsystem. FIG. 1A shows an overview of phage-assisted continuous evolution(PACE). FIG. 1B shows a reporter system used to couple DNA binding toinduction of gene III-luciferase expression. FIG. 1C shows theluciferase activity resulting from ATc-induced Zif268 protein binding toeither its on-target sequence (5′-GCGTGGGCG-′3; SEQ ID NO: 48) or anoff-target sequence (5′-GCGTTAGCG-′3; SEQ ID NO: 49). FIG. 1D shows theluciferase activity resulting from ATc-induced TALE protein binding toeither its on-target sequence (CBX8: 5′-TTCAGGAGGGCTTCGGC-3′, SEQ ID NO:36) or an off-target sequence (5′-TTCATAAGGGATTAGGC-3′, SEQ ID NO: 40).Bar graphs in FIGS. 1C and 1D represent mean+s.d. (n=3).

FIGS. 2A-2D show the continuous evolution of TALEs with altered 5′ basespecificity. FIG. 2A shows the CBX8-targeting TALE-w fusion and therelationship between individual repeats and target sequence nucleotides.The sequences correspond to SEQ ID NOs: 36-39. FIG. 2B shows theluciferase activity shown as fold induction from TALE induction(relative to controls lacking induction of TALE expression) for thecanonical TALE and five evolved clones from either lagoon 1 (L) orlagoon 2 (L2) using a CBX8 target sequence variant beginning with 5′ A(left). The right panel of FIG. 2B also shows mutations in the evolvedproteins shown in the left panel. Blue squares indicate mutations withinthe TALE domain, and green squares indicate mutations within the cosubunit. FIG. 2C shows the reporter system used to couple DNA binding toan off-target sequence to production of pIII-neg-YFP. The left panel ofFIG. 2D shows YFP fluorescence represented as fold induction uponinduction of TALE expression, for the canonical TALE and two evolvedclones from either L1 or L2 using CBX8-target sequences beginning with5′ A, 5′ C, 5′ G, or 5′ T. The right panel of FIG. 2D shows themutations in the evolved proteins shown in the left panel. Bar graphs inFIGS. 2B and 2D represent mean+s.d. (n=3).

FIGS. 3A-3B show the continuous evolution of TALEs with improvedspecificity. FIG. 3A shows a schematic of the ATM targeting TALE-ωfusion and the relationship between individual TALE repeats and thenucleotides they recognize for the on-target sequence (ATM:5′-TGAATTGGGATGCTGTTT-3′ (SEQ ID NO: 15)), or the most highly cleavedhuman genomic off-target sequence (OffA17: 5′-GGAAATGGGATACTGAGT-3′ (SEQID NO: 21)). The left panel of FIG. 3B shows the relative cleavageefficiencies of the canonical ATM TALEN pair or four ATM TALEN pairscontaining the canonical ATM-right half site TALEN and an evolvedATM-left half site TALEN (L1-2, L2-1, L3-1, or L3-2) on a linear 6-kbDNA fragment containing either the ATM on-target sequence or the OffA17off-target sequence. The top band is non-cleaved DNA, while the bottomband is a cleavage product. Cleavage percentages were determined usingdensitometry analysis (GelEval), and are included below each lane. Theright panel of FIG. 3B shows mutations in the evolved ATM-left half siteTALEs used in the left panel.

FIGS. 4A-4D show high-throughput specificity profiling of canonical andevolved TALENs. In FIGS. 4A and 4B, the top panels are heat maps showingspecificity scores for either canonical (FIG. 4A) or L3-1 (FIG. 4B)evolved TALENs targeting the ATM locus at each position in the left andright half-sites plus a single flanking position (N). In FIGS. 4A and4B, the bottom panels are bar graphs showing the quantitativespecificity score for each nucleotide position. A score of zeroindicates no specificity, while a score of 1.0 corresponds to perfectspecificity. The sequences in FIG. 4A correspond to SEQ ID NO: 50 (left)and SEQ ID NO: 51 (right). The sequences in FIG. 4B correspond to SEQ IDNO: 50 (left) and SEQ ID NO: 51 (right). FIG. 4C is a bar graphindicating the quantitative difference in specificity score at eachposition between the canonical and L3-1 evolved TALENs(score_(L3-1)-score_(canonical)) at each position in the targethalf-sites plus a single flanking position (N). A score of zeroindicates no change in specificity. The sequences in FIG. 4C correspondto SEQ ID NO: 15 (left) and SEQ ID NO: 16 (right). For all heat maps,the cognate base for each position in the target sequence is boxed. Forthe right half-site, data for the sense strand are displayed. FIG. 4D isidentical to FIG. 4C, except for the L3-2 evolved TALEN versus thecanonical TALEN. The sequences in FIG. 4D correspond to SEQ ID NO: 15(left) and SEQ ID NO: 16 (right).

FIG. 5 shows the optimization of a one-hybrid architecture for PACE.Comparison of pIII-luciferase fold induction (ATc-induced Zif268expression/non-induced luminescence) resulting from binding of a Zif268fusion with either the α or ω subunit of RNAP to a Zif268 operatorsequence (5′-GCGTGGGCG-3′; SEQ ID NO: 48) centered at either −55 or −62.M refers to a medium-length linker between Zif268 and the RNAP subunit(AAATSGGGGAA (SEQ ID NO: 52)), and L refers to a longer linker(AAGGGGSGGGGSGGGGSTAAA (SEQ ID NO: 53)). Data represent mean+s.d. (n=3).

FIGS. 6A-6B show that chromosomal pspBC deletion enables small-moleculecontrol of the phage shock promoter response. FIG. 6A shows a comparisonof phage-shock promoter response between S1030 and S1632 cells. Uponphage infection, activation of a phage shock promoter (PSP) inducesbacterial luciferase expression, and can be measured as an increase inluminescence. The phage shock response sensors pspBC were deleted fromS1632 cells, resulting in no transcriptional activation in the absenceor presence of infecting phage. FIG. 6B shows that the over-expressionof pspBC from an arabinose-controlled promoter (P_(BAD)) results inactivation of the PSP in a manner independent of phage infection,eliminating variability in transcriptional activation of the promoter.Data represent mean±s.d. (n=3).

FIGS. 7A-7C show the generation of mutant PSP variants with altereddynamic range. Mutants abrogating the efficiency or backgroundtranscription of the PSP were constructed and tested through low-levelexpression of the phage shock sensors pspBC, which are master inducersof the phage shock response. Mutations were constructed based on priorknowledge of the PSP architecture⁵⁷ and σ54 promoter activities⁵⁸.Generally, mutations were focused on the 054 core promoter. The “AR”series carried additional mutations to reduce the strength of 070cryptic promoters that may influence background transcription levels.FIG. 7A shows the luminescence signal in the presence or absence of 20μM arabinose from wild-type and mutant PSP promoters. All readings werenormalized to wild-type PSP, which was set to 1. Data representmean±s.d. (n=3). FIG. 7B-7C present a summary of activity, backgroundlevels, and genotypes of mutant promoters assayed in FIG. 7A. Backgroundlevels of all mutant promoters are listed relative to wild-type (SEQ IDNO: 65).

FIGS. 8A-8C show the generation of S2060, a bacterial strain forchaperone overexpression and robust visualization of phage plaques. FIG.8A shows the luminescence resulting from induction of a bacterialluciferase (luxAB) cassette driven by the P_(lux) promoter in responseto the indicated doses of N-(3-oxohexanoyl)-1-homoserine lactone (OHHL)(the LuxR transcriptional regulator is also controlled by the P_(lux)promoter, only in the opposite direction). Data represent mean±s.d.(n=3). FIG. 8B shows the kinetic analysis of OHHL-mediated expression ofGroESL (cassette: luxR-P_(lux)-groESL) on the folding of LuxAB(cassette: araC-P_(BAD)-LuxAB), a known substrate for GroESL. Increasedin vivo concentrations of GroESL result in improved folding of LuxAB andrapid saturation of the luminescence response. FIG. 8C shows acomparison of the ability to visualize plaque formation using S1030,S2058, S2059, and S2060 cells. Chromosomally identical strains lacking(S1030) or carrying the lacZ and groESL cassettes (S2058, S2059, S2060)were infected with WT M13 bacteriophage. The modified strains carry thewild-type (WT) PSP, PSP-T1 or PSP-AR2, respectively. The reducedbackground and maintained transcriptional activation of the T1 and AR2variants enables the visualization of phage plaques in top agarsupplemented with Bluo-Gal, an X-Gal derivative.

FIGS. 9A-9D show the continuous propagation of Zif268 in PACE, andreversion of an inactive Zif268 mutant to wild-type. FIG. 9A showsplaque assays of Zif268-SP or a control SP encoding T7 RNAP instead ofZif268 on S2060 cells containing APs encoding either the on- oroff-target sequence, or S2208 cells (positive control). FIG. 9B is aschematic of the relative location of genes in the Zif268-SP, and asummary of mutations arising following 24 h of PACE to optimize thephage backbone and one-hybrid system. FIG. 9C shows the plaque assayresults for wild-type Zif268-SP, inactive mutant Zif268-R24V-SP, andevolved SPs derived from a 24 h drift/24 h PACE experiment in thepresence of mutagenesis. ‘+’ denotes the presence of plaques, while ‘-’denotes the absence of plaques. FIG. 9D shows the genotypes of fivephage clones isolated following PACE, all displaying reversion of V24 toR. The nucleic acid sequences in FIG. 9D, from top to bottom, correspondto wild-type (SEQ ID NO: 54), initial (SEQ ID NO: 55) and PACE (SEQ IDNO: 56). The amino acid sequences in FIG. 9D, from top to bottom,correspond to SEQ ID NO: 57, SEQ ID NO: 58, and SEQ ID NO: 57.

FIGS. 10A-10D show the optimization of a TALE one-hybrid architecturefor PACE. FIG. 10A shows a comparison of pIII-luciferase fold induction(ATc-induced TALE/noninduced luminescence) resulting from binding of aCBX8-targeting TALE-w fusion construct to the cognate operator sequence(5′-TTCAGGAGGGCTTCGGC-′3 (SEQ ID NO: 36)) centered at −62. The length ofthe natural TALE C-terminus used as a linker to the co subunit isindicated. G4S represents the addition of a GGGGS sequence to the end ofthe C-terminal fragment to increase the flexibility of the linker. Datarepresent mean+s.d. (n=3). FIG. 10B shows the plaque assays of TALE-SPor a control SP encoding T7 RNA polymerase instead of a TALE on S2060cells containing APs with either the on- or off-target sequence, or onS2208 cells (positive control). FIG. 10C is a schematic of the locationof genes contained in a CBX8-TALE-SP plasmid, and a summary of evolvedmutations following 24 h of PACE. FIG. 10D depicts pIII-luciferase foldinduction (ATc-induced TALE/non-induced luminescence) by binding of aCBX8-targeting TALE-w to CBX8-binding sequences beginning with 5′ A, C,G, or T. Data represent mean+s.d. (n=3).

FIGS. 11A-11B show the evolution of CBX8-TALE variants with increasedactivity towards 5′ C or 5′ G sequences. The left panel of FIG. 11Adepicts luciferase activity shown as fold induction (ATc-induced TALEluminescence/non-induced luminescence) for the canonical TALE (inputTALE) and five PACE-evolved clones from either lagoon 1 (L1) or lagoon 2(L2) evolved to bind a CBX8-target sequence beginning with 5′ C. Theright panel of FIG. 11A shows the genotypes for the clones shown in theleft panel. The left panel in FIG. 11B is identical to FIG. 11A, butwith clones evolved to bind a CBX8-target sequence beginning with 5′ G.The right panel of FIG. 11B shows genotypes for the clones shown in theleft panel. For FIGS. 11A-11B, blue shaded squares indicate mutationswithin the TALE domain, and green shaded squares indicate mutationswithin the co subunit, and data show mean+s.d. (n=3).

FIGS. 12A-12C show high-throughput sequence analysis of phagepopulations evolved to bind target sequences beginning with 5′ A, C, orG. Frequency of mutations arising in lagoon 1 (L) or lagoon 2 (L2)following 48 h of PACE in the presence of mutagenesis on CBX8-directedtarget sequences beginning with 5′ A (FIG. 12A), 5′ C (FIG. 12B), or 5′G (FIG. 12C). Only mutations observed at a frequency >5% are shown.

FIGS. 13A-13H show characterizations of the mutations arising from theevolution towards 5′ A, C, or G target sequence binding. FIG. 13A showsthe location of mutations with >5% prevalence in the populationidentified in 5′ A, C, or G evolutions within the core TALE unit (SEQ IDNO: 66). ‘Multiple’ refers to equivalent mutations identified inmultiple different repeats either in the same experiment or in aseparate experiment. FIG. 13B shows luciferase activity represented asfold induction (ATc-induced TALE luminescence/non-induced luminescence)for the canonical TALE and five mutant constructs using a 5′ ACBX8-target sequence. FIG. 13C presents the crystal structure⁴⁸ showingthe location of A133, A79, and W120. The corresponding number for eachresidue in the crystal structure⁴⁸ is shown in parenthesis. FIG. 13Dshows luciferase activity represented as fold induction (ATc-inducedTALE luminescence/non-induced luminescence) for the a CBX8-directed TALEwith an A79E mutation on CBX8-directed target sequences beginning with5′ A, C, G, or T. FIG. 13E presents the crystal structure⁴⁹ indicatingthe position of the C-terminal residue Q711. Numbering corresponding tothe original crystal structure⁴⁹ is shown in parenthesis. Crystalstructure⁴⁹ of three TALE repeats showing the positions of the L508(FIG. 13F), E622 (FIG. 13G), and K634 (FIG. 13H) residues within a coreTALE repeat (repeat in light shading, residues in dark shading). Bargraphs in FIGS. 13B and 13D represent mean+s.d. (n=3).

FIGS. 14A-14C show the specificity of phage evolved to recognize 5′ A,C, or G. and negative selection validation. FIG. 14A shows the resultsof plaque assays of phage pools evolved on CBX8-directed targetsequences beginning with 5′ A, C, or, G on S1059 cells (positivecontrol), or S1030 cells carrying no APs (negative control), or S1030cells carrying AP containing target sequences beginning with 5′ A, C, G,or T. FIG. 14B presents plaque assays using phage evolved to bind a 5′ Atarget sequence on S1030 cells carrying the indicated combinations ofAP/APNeg plasmids in the presence of increasing doses of theophylline.FIG. 14C shows the results of a similar experiment to FIG. 14B usingdifferent doses of theophylline. ‘-’ indicates no plaque formation, ‘+’indicates weak plaque formation, ‘++’ indicates moderate plaqueformation, and ‘+++’ indicates strong phage plaque formation.

FIGS. 15A-15B show clonal and population genotypes following negativeselection of 5′ A-evolved phage against 5′ C, G, and T binding. FIG. 15Ashows the genotypes of five evolved phage clones from lagoon 1 or lagoon2 following 144 h of PACE under positive selection for 5′ A binding, andnegative selection against CBX8-target sequences beginning with 5′ C, G,or T. Light shaded squares indicate mutations within the TALE domain,and dark shaded squares indicate mutations within the co subunit. FIG.15B shows mutations arising in lagoon 1 (L) or lagoon 2 (L2) following144 h of dual positive and negative selection PACE. Only mutationsarising at a frequency of >5% are shown.

FIGS. 16A-16D show a characterization of mutations arising from negativeselection PACE against target sequences beginning with 5′ C, G, or T.FIG. 16A depicts the crystal structure⁴⁹ showing the location of K59 andW120. The corresponding number for each residue in the crystal structureis shown in parenthesis. FIG. 16B depicts the crystal structure⁴⁹ ofthree TALE repeats showing the relative position of the Q513 (repeat inlight shading, residue in dark shading). FIG. 16C shows the luciferaseactivity represented as fold induction (ATc-induced TALEluminescence/non-induced luminescence) for the canonical CBX8-directedTALE or a K59E mutant protein on CBX8-directed target sequencesbeginning with 5′ A, C, G, or T. FIG. 16D shows the luciferase activityrepresented as fold induction (ATc-induced TALE luminescence/non-inducedluminescence for the indicated doses of ATc) for the canonicalATM-L-directed TALE or a K59E mutant protein on ATM-L directed targetsequences beginning with 5′ A, C, G, or T. Data represent mean+s.d.(n=3).

FIGS. 17A-17B present a comparison of on=target cleavage efficiency ofcanonical and evolved L3-2 TALENs. FIG. 17A depicts TALEN dose titrationshowing the relative cleavage efficiencies of the canonical ATM TALENpair or the L3-2 TALEN on 50 ng (˜0.75 nM) of a linear 6-kb DNA fragmentcontaining the ATM on-target sequence (ATM: 5′-TGAATTGGGATGCTGTTT-3′(SEQ ID NO: 15)). The top band is non-cleaved DNA, while the bottom bandis a cleavage product. Quantified cleavage percentages were determinedusing densitometry (GelEval), and are shown below each lane. FIG. 17Bshows DNA cleavage saturation curves for the canonical ATM TALEN pairand the TALEN pair containing the evolved L3-2 TALE. An in vitrocleavage assay was performed to measure DNA cleavage of 0.5 ng of DNAcontaining the ATM on-target sequence (˜7.5 pM) by either the canonicalTALEN pair or the L3-2 TALEN pair at concentrations of 0.01, 0.04, 0.12,0.37, 1.11, 3.33, or 10 nM. The amount of uncleaved DNA remaining afterthe reaction was quantified by qPCR. Fraction cleaved DNA was calculatedas the amount of cleaved DNA present following completion of eachcleavage reaction divided by the total amount of DNA input into eachreaction.

FIGS. 18A-18D show characterizations of evolved ATM-L TALEs followingpositive and negative selection PACE. FIG. 18A shows the luciferaseactivity represented as fold induction (ATc-induced TALEluminescence/non-induced luminescence) for the canonical ATM-L-directedTALE or L3-1 and L3-2, on the on-target sequence (ATM:5′-TGAATTGGGATGCTGTTT-3′ (SEQ ID NO: 15)), or on the off-target sequenceOffA17 (OffA17: 5′-GGAAATGGGATACTGAGT-3′ (SEQ ID NO: 21)). Datarepresent mean+s.d. (n=3). FIGS. 18B-18C show the genotypes ofindividual evolved phage clones following dual positive and negativeselection PACE (against OffA17). Light shaded squares indicate mutationswithin the TALE domain, and dark shaded squares indicate mutationswithin the co subunit. The left panel of FIG. 18D shows the relativecleavage efficiencies of the canonical ATM TALEN pair or two TALENscontaining an evolved left half-site (L1-1, or L3-2) on a linear 6-kbDNA fragment containing either the ATM on-target sequence or the OffA17off-target sequence. The top band is non-cleaved DNA, while the bottomband is a cleavage product. Quantified cleavage percentages weredetermined using densitometry (GelEval), and are shown below each lane.The right panel of FIG. 18D shows mutations in the evolved ATM-left halfsite TALEs used in the left panel.

FIGS. 19A-19F show the characterization of mutations identified inpositive and negative selection ATM-L TALE PACE and evolved TALENspecificity. Relative cleavage efficiencies of the canonical ATM TALENpair, or a TALEN (L1-2) containing an evolved left half-site TALE withthe A252T mutation and the canonical right half-site TALE on a linear6-kb DNA fragment containing either the ATM on-target sequence or theOffA17 off-target sequence (FIG. 19A). The top band is non-cleaved DNA,while the bottom band is a cleavage product. FIG. 19B is the same as inFIG. 19A, but assaying a TALEN containing a Q745P substitution. Crystalstructure⁴⁹ of three TALE repeats showing the relative positions of theA252 (FIG. 19C), and L338 (FIG. 19D) residues within a core TALE repeat(repeat in light shading, residues in dark shading). FIG. 19E shows therelative cleavage efficiencies of the canonical ATM TALEN pair, or aTALEN (L3-1) containing an evolved left half-site on a linear 6-kb DNAfragment containing either the ATM on-target sequence, the OffA17sequence, or a derivative of the OffA17 sequence containing a subset ofits 5 mutations (D1-D4 listed in the figure). The sequences, from top tobottom, correspond to SEQ ID NOs: 15, 21, and 67-70. FIG. 19F is thesame as in FIG. 19E, but with derivative sequences containing fewermutations relative to the on-target sequence (1 or 2 bp). The sequences,from top to bottom, correspond to SEQ ID NOs: 15, 71-74. For allcleavage gels, the top band is non-cleaved DNA, while the bottom band isa cleavage product. Quantified cleavage percentages were determinedusing densitometry (GelEval), and are shown below each lane.

FIGS. 20A-20B show a global analysis of in vitro TALEN specificity. FIG.20A shows sequences surviving selection (TALEN digestion) compared tothe pre-selection library as a function of the number of mutations inboth half-sites (left and right half-sites combined excluding thespacer) for each of the ten reaction conditions listed. FIG. 20B showsthe enrichment value of on-target (no mutations) and off-targetsequences containing one to nine mutations in both half sites (left andright half-sites combined excluding the spacer) for each of the tenreaction conditions listed.

FIGS. 21A-21D are specificity profile heat maps for the canonical ATMTALEN pair as a function of concentration. Heat maps showing specificityscores for the canonical TALEN targeting the ATM locus used in thecleavage assay at doses of 20 nM (FIG. 21A), 10 nM (FIG. 21B), 5 nM(FIG. 21C), and 2.5 nM (FIG. 21D). Each position in the left and righthalf-sites plus a single flanking position (N) are shown. Colors rangefrom dark shading at a score of 1.0 (complete specificity), to white ata score of 0 (no specificity), to dark shading at a score of −1.0(maximum negative score). The cognate base for each position in thetarget sequence is boxed. For the right half-site, data for the sensestrand are displayed. The sequences, from left to right, correspond toSEQ ID NOs: 50 and 51.

FIGS. 22A-22D are specificity profile bar graphs of the canonical ATMTALEN pair as a function of concentration. Bar graphs showing thequantitative specificity score for each nucleotide position for thecanonical TALEN targeting the ATM locus used in the cleavage assay atdoses of 20 nM (FIG. 22A), 10 nM (FIG. 22B), 5 nM (FIG. 22C), and 2.5 nM(FIG. 22D). Each position in the left and right half-sites plus a singleflanking position (N) are shown. A score of zero indicates nospecificity, while a score of 1.0 corresponds to perfect specificity.Negative specificity scores range from zero to −1.0, and representenrichment against that base pair. Specified positions (specificityscore >0) were plotted as stacked bars above the axis (multiplespecified base pairs at the same position were plotted over each otherwith the shortest bar in front) while anti-specified base pairs wereplotted as narrow, grouped bars below the axis. For the right half-site,data for the sense strand are displayed. The sequences, from left toright, correspond to SEQ ID NOs: 50 and 51.

FIGS. 23A-23F are the specificity profile heat maps of L2-1, L3-1, andL3-2 ATM TALEN pairs. Heat maps showing specificity scores for the L3-1TALEN pair at doses of 20 nM (FIG. 23A), 10 nM (FIG. 23B), 5 nM (FIG.23C), and 2.5 nM (FIG. 23D), or TALEN pairs incorporating L3-2 and L2-1TALEs at a dose of 10 nM (FIGS. 23E and 23F, respectively). Eachposition in the left and right half-sites plus a single flankingposition (N) are shown. Colors range from dark shading at a score of 1.0(complete specificity), to white at a score of 0 (no specificity), todark shading at a score of −1.0 (maximum negative score). The cognatebase for each position in the target sequence is boxed. For the righthalf-site, data for the sense strand are displayed. The sequences, fromleft to right, correspond to SEQ ID NOs: 50 and 51.

FIGS. 24A-24F are the specificity profile bar graphs of L2-1, L3-1, andL3-2 ATM TALEN pairs. Bar graphs showing the quantitative specificityscore for each nucleotide position for the L3-1 TALEN pair at doses of20 nM (FIG. 24A), 10 nM (FIG. 24B), 5 nM (FIG. 24C), and 2.5 nM (FIG.24D), or TALEN pairs incorporating L3-2 and L2-1 TALEs at a dose of 10Nm (FIGS. 24E and 24F, respectively). Each position in the left andright half-sites plus a single flanking position (N) are shown. A scoreof zero indicates no specificity, while a score of 1.0 corresponds toperfect specificity. Negative specificity scores range from zero to−1.0, and represent enrichment against that base pair. Specifiedpositions (specificity score >0) were plotted as stacked bars above theaxis (multiple specified base pairs at the same position were plottedover each other with the shortest bar in front) while antispecified basepairs were plotted as narrow, grouped bars below the axis. For the righthalf-site, data for the sense strand are displayed. The sequences, fromleft to right, correspond to SEQ ID NOs: 50 and 51.

FIGS. 25A-25F show specificity profile difference as a function of TALENconcentration for canonical and L3-1 ATM TALEN pairs. Bar graphindicating the quantitative difference in specificity score at eachposition between cleavage using the canonical TALEN pair at a dose of 20nM and 10 nM (FIG. 25A), 5 nM (FIG. 25B), and 2.5 nM (calculated asscore_(lowdose)-score_(20 nM)) (FIG. 25C), or TALEN pairs incorporatingan evolved L3-1 ATM TALE at a dose of 20 nM and 10 nM (FIG. 25D), 5 nM(FIG. 25E), and 2.5 nM (FIG. 25F). A score of zero indicates no changein specificity. For the right half-site, data for the sense strand aredisplayed. The sequences, from left to right, correspond to SEQ ID NOs:15 and 16.

FIGS. 26A-26C are bar graphs showing the difference in specificity ofthe canonical TALEN pair versus the L2-1, L3-1, and L3-2 TALEN pairs.Bar graph indicating the quantitative difference in specificity score ateach position between cleavage using the canonical TALEN pair or TALENsincorporating L3-1 (FIG. 26A) or L3-2 (FIG. 26B), or L2-1 (FIG. 26C)TALEs, all at a dose of 10 nM. Difference scores were calculated asscore_(L2/3)-score_(WT). Bases at each position in the target half-sitesare displayed. A score of zero indicates no change in specificity. Forthe right half-site, data for the sense strand are displayed. Thesequences, from left to right, correspond to SEQ ID NOs: 15 and 16.

FIG. 27 shows the specificity of a CCR5-targeting TALE in the DB-PACEone-hybrid system. Luciferase activity represented as fold induction(ATc-induced TALE luminescence/non-induced luminescence) for a canonicalCCR5-R-directed TALE on its on-target sequence or one of threepreviously described off-target sequences³⁰ (Off-5, Off-15, Off-28;sequences indicated in the figure). Data represent mean+s.d. (n=3). Thesequences, from top to bottom, correspond to SEQ ID NOs: 59-62.

DEFINITIONS

The term “canonical sequence,” as used herein, refers to a sequence ofDNA, RNA, or amino acids that reflects a common choice of base or aminoacid at each position amongst known molecules of that type. For example,the canonical amino acid sequence of a protein domain may reflect themost common choice of amino acid resides at each position amongst allknown domains of that type, or amongst the majority of known domains ofthat type.

The terms “conjugating,” “conjugated,” and “conjugation” refer to anassociation of two entities, for example, of two molecules such as twoproteins, two domains (e.g., a binding domain and a cleavage domain), ora protein and an agent (e.g., a protein binding domain and a smallmolecule). The association can be, for example, via a direct or indirect(e.g., via a linker) covalent linkage or via non-covalent interactions.In some embodiments, the association is covalent. In some embodiments,two molecules are conjugated via a linker connecting both molecules. Forexample, in some embodiments where two proteins are conjugated to eachother, e.g., a binding domain and a cleavage domain of an engineerednuclease, to form a protein fusion, the two proteins may be conjugatedvia a polypeptide linker, e.g., an amino acid sequence connecting theC-terminus of one protein to the N-terminus of the other protein.

The term “effective amount,” as used herein, refers to an amount of abiologically active agent that is sufficient to elicit a desiredbiological response. For example, in some embodiments, an effectiveamount of a TALE nuclease may refer to the amount of the nuclease thatis sufficient to induce cleavage of a target site specifically bound andcleaved by the nuclease, e.g., in a cell-free assay, or in a targetcell, tissue, or organism. As will be appreciated by the skilledartisan, the effective amount of an agent, e.g., a nuclease, a hybridprotein, or a polynucleotide, may vary depending on various factors as,for example, on the desired biological response, the specific allele,genome, target site, cell, or tissue being targeted, and the agent beingused.

The term “engineered,” as used herein, refers to a molecule, complex,substance, or entity that has been designed, produced, prepared,synthesized, and/or manufactured by a human. Accordingly, an engineeredproduct is a product that does not occur in nature. In some embodiments,an engineered molecule or complex, e.g., an engineered TALEN monomer,dimer, or multimer, is a TALEN that has been designed to meet particularrequirements or to have particular desired features e.g., tospecifically bind a target sequence of interest with minimal off-targetbinding, to have a specific minimal or maximal cleavage activity, and/orto have a specific stability.

The term “homology,” as used herein, refers to the overall relatednessbetween nucleic acids (e.g. DNA molecules and/or RNA molecules) orpolypeptides. In some embodiments, two amino acid sequences areconsidered to be homologous if the amino acid sequences are at leastabout 50% identical, at least about 55% identical, at least about 60%identical, at least about 65% identical, at least about 70% identical,at least about 75% identical, at least about 80% identical, at leastabout 85% identical, at least about 90% identical, at least about 95%identical, at least about 96% identical, at least about 98% identical,or at least about 99% identical for at least one stretch of at leastabout 20 contiguous amino acids. Those of skill in the art will be awareof suitable methods for aligning and determining homology between twonucleic acid or amino acid sequences. Exemplary suitable methodsinclude, without limitation, those described in Computational MolecularBiology, Lesk, A. M., ed., Oxford University Press, New York, 1988;Biocomputing: Informatics and Genome Projects, Smith, D. W., ed.,Academic Press, New York, 1993; Sequence Analysis in Molecular Biology,von Heinje, G., Academic Press, 1987; Computer Analysis of SequenceData, Part I, Griffin, A. M., and Griffin, H. G., eds., Humana Press,New Jersey, 1994; and Sequence Analysis Primer, Gribskov, M. andDevereux, J., eds., M Stockton Press, New York, 1991; the entirecontents of each of which are incorporated herein by reference. Forexample, the percent identity between two nucleotide sequences can bedetermined using the algorithm of Meyers and Miller (CABIOS, 1989,4:11-17), which has been incorporated into the ALIGN program (version2.0) using a PAM120 weight residue table, a gap length penalty of 12 anda gap penalty of 4. The percent identity between two nucleotidesequences can also be determined using the GAP program in the GCGsoftware package using an NWSgapdna.CMP matrix. Additional exemplarysuitable methods commonly employed to determine percent identity betweensequences include, but are not limited to those disclosed in Carillo,H., and Lipman, D., SIAM J Applied Math., 48:1073 (1988); incorporatedherein by reference. Exemplary suitable computer software to determinehomology between two sequences include, but are not limited to, GCGprogram package, Devereux, J., et al., Nucleic Acids Research, 12(1),387 (1984)), BLASTP, BLASTN, and FASTA Atschul, S. F. et al., J. Molec.Biol., 215, 403 (1990)).

The term “linker,” as used herein, refers to a chemical group or amolecule linking two molecules or moieties, e.g., a binding domain and acleavage domain of a TALE nuclease. Typically, the linker is positionedbetween, or flanked by, two groups, molecules, or other moieties andconnected to each one via a covalent bond, thus connecting the two. Insome embodiments, the linker is an amino acid or a plurality of aminoacids (e.g., a peptide or protein). In some embodiments, the linker isan organic molecule, group, polymer, or chemical moiety.

The term “nuclease,” as used herein, refers to an agent, for example, aprotein or a nucleic acid molecule, capable of cleaving a phosphodiesterbond connecting nucleotide residues in a nucleic acid molecule. In someembodiments, a nuclease is a protein, e.g., an enzyme or enzyme domainthat can bind a nucleic acid molecule and cleave a phosphodiester bondconnecting nucleotide residues within the nucleic acid molecule. Anuclease may be an endonuclease, cleaving a phosphodiester bonds withina polynucleotide chain, or an exonuclease, cleaving a phosphodiesterbond at the end of the polynucleotide chain. In some embodiments, anuclease site-specific nuclease, binding and/or cleaving a specificphosphodiester bond within a specific nucleotide sequence, which is alsoreferred to herein as the “recognition sequence,” the “nuclease targetsite,” or the “target site.” The nuclease, in some embodiments,comprises a nuclease domain from a naturally-occurring nuclease. In someembodiments, the nuclease comprises a nuclease domain from anon-naturally-occurring nuclease. In some embodiments, the nucleasecomprises a nuclease domain from a meganuclease, a zinc finger nuclease,a TALE nuclease (TALEN), or a restriction endonuclease (e.g., FokI,EcoRI, HindIII, or BamHI). The nucleases and nuclease domains providedherein are exemplary and meant to illustrate some embodiments, but arenot meant to be limiting. Those of ordinary skill in the art will beaware of additional suitable nucleases and nuclease domains.

A nuclease protein typically comprises a “binding domain” that mediatesthe interaction of the protein with the nucleic acid substrate, and a“cleavage domain” that catalyzes the cleavage of the phosphodiester bondwithin the nucleic acid backbone. In some embodiments, a nucleaseprotein can bind and cleave a nucleic acid molecule in a monomeric form,while, in other embodiments, a nuclease protein has to dimerize ormultimerize in order to cleave a target nucleic acid molecule. Bindingdomains and cleavage domains of naturally occurring nucleases, as wellas modular binding domains and cleavage domains that can be combined tocreate nucleases that bind specific target sites, are well known tothose of skill in the art. For example, transcriptional activator likeelements can be used as binding domains to specifically bind a desiredtarget site, and fused or conjugated to a cleavage domain, for example,the cleavage domain of FokI, to create an engineered nuclease cleavingthe desired target site.

The terms “nucleic acid” and “nucleic acid molecule,” as used herein,refer to a compound comprising a nucleobase and an acidic moiety, e.g.,a nucleoside, a nucleotide, or a polymer of nucleotides. Typically,polymeric nucleic acids, e.g., nucleic acid molecules comprising threeor more nucleotides are linear molecules, in which adjacent nucleotidesare linked to each other via a phosphodiester linkage. In someembodiments, “nucleic acid” refers to individual nucleic acid residues(e.g. nucleotides and/or nucleosides). In some embodiments, “nucleicacid” refers to an oligonucleotide chain comprising three or moreindividual nucleotide residues. As used herein, the terms“oligonucleotide” and “polynucleotide” can be used interchangeably torefer to a polymer of nucleotides (e.g., a string of at least threenucleotides). In some embodiments, “nucleic acid” encompasses RNA aswell as single and/or double-stranded DNA. Nucleic acids may benaturally occurring, for example, in the context of a genome, atranscript, an mRNA, tRNA, rRNA, siRNA, snRNA, a plasmid, cosmid,chromosome, chromatid, or other naturally occurring nucleic acidmolecule. On the other hand, a nucleic acid molecule may be anon-naturally occurring molecule, e.g., a recombinant DNA or RNA, anartificial chromosome, an engineered genome, or fragment thereof, or asynthetic DNA, RNA, DNA/RNA hybrid, or including non-naturally occurringnucleotides or nucleosides. Furthermore, the terms “nucleic acid,”“DNA,” “RNA,” and/or similar terms include nucleic acid analogs, e.g.,analogs having other than a phosphodiester backbone. Nucleic acids canbe purified from natural sources, produced using recombinant expressionsystems and optionally purified, chemically synthesized, etc. Whereappropriate, e.g., in the case of chemically synthesized molecules,nucleic acids can comprise nucleoside analogs such as analogs havingchemically modified bases or sugars, and backbone modifications' Anucleic acid sequence is presented in the 5′ to 3′ direction unlessotherwise indicated. In some embodiments, a nucleic acid is or comprisesnatural nucleosides (e.g. adenosine, thymidine, guanosine, cytidine,uridine, deoxyadenosine, deoxythymidine, deoxyguanosine, anddeoxycytidine); nucleoside analogs (e.g., 2-aminoadenosine,2-thiothymidine, inosine, pyrrolo-pyrimidine, 3-methyl adenosine,5-methylcytidine, 2-aminoadenosine, C5-bromouridine, C5-fluorouridine,C5-iodouridine, C5-propynyl-uridine, C5-propynyl-cytidine,C5-methylcytidine, 2-aminoadenosine, 7-deazaadenosine, 7-deazaguanosine,8-oxoadenosine, 8-oxoguanosine, O(6)-methylguanine, and 2-thiocytidine);chemically modified bases; biologically modified bases (e.g., methylatedbases); intercalated bases; modified sugars (e.g., 2′-fluororibose,ribose, 2′-deoxyribose, arabinose, and hexose); and/or modifiedphosphate groups (e.g., phosphorothioates and 5′-N-phosphoramiditelinkages).

The term “pharmaceutical composition,” as used herein, refers to acomposition that can be administrated to a subject in the context oftreatment of a disease or disorder. In some embodiments, apharmaceutical composition comprises an active ingredient, e.g. anuclease or a nucleic acid encoding a nuclease, and a pharmaceuticallyacceptable excipient.

The terms “prevention” or “prevent” refer to the prophylactic treatmentof a subject who is at risk of developing a disease, disorder, orcondition (e.g., at an elevated risk as compared to a control subject,or a control group of subject, or at an elevated risk as compared to theaverage risk of an age-matched and/or gender-matched subject), resultingin a decrease in the probability that the subject will develop thedisease, disorder, or condition (as compared to the probability withoutprevention), and/or to the inhibition of further advancement of analready established disorder.

The term “proliferative disease,” as used herein, refers to any diseasein which cell or tissue homeostasis is disturbed in that a cell or cellpopulation exhibits an abnormally elevated proliferation rate.Proliferative diseases include hyperproliferative diseases, such aspre-neoplastic hyperplastic conditions and neoplastic diseases.Neoplastic diseases are characterized by an abnormal proliferation ofcells and include both benign and malignant neoplasias. Malignantneoplasms are also referred to as cancers.

The terms “protein,” “peptide,” and “polypeptide” are usedinterchangeably herein and refer to a polymer of amino acid residueslinked together by peptide (amide) bonds. The terms refer to a protein,peptide, or polypeptide of any size, structure, or function. Typically,a protein, peptide, or polypeptide will be at least three amino acidslong. A protein, peptide, or polypeptide may refer to an individualprotein or a collection of proteins. One or more of the amino acids in aprotein, peptide, or polypeptide may be modified, for example, by theaddition of a chemical entity such as a carbohydrate group, a hydroxylgroup, a phosphate group, a farnesyl group, an isofarnesyl group, afatty acid group, a linker for conjugation, functionalization, or othermodification, etc. A protein, peptide, or polypeptide may also be asingle molecule or may be a multi-molecular complex. A protein maycomprise different domains, for example, a nucleic acid binding domainand a nucleic acid cleavage domain. In some embodiments, a proteincomprises a proteinaceous part, e.g., an amino acid sequenceconstituting a nucleic acid binding domain, and an organic compound,e.g., a compound that can act as a nucleic acid cleavage agent.

The term “subject,” as used herein, refers to an individual organism,for example, an individual mammal. In some embodiments, the subject is ahuman. In some embodiments, the subject is a non-human mammal. In someembodiments, the subject is a non-human primate. In some embodiments,the subject is a rodent. In some embodiments, the subject is a sheep, agoat, a cattle, a cat, or a dog. In some embodiments, the subject is avertebrate, an amphibian, a reptile, a fish, an insect, a fly, or anematode.

The term “target site,” used herein interchangeably with the term“nuclease target site,” refers to a sequence within a nucleic acidmolecule that a TALE binds to. A target site may be single-stranded ordouble-stranded. In the context of nucleases that dimerize, e.g., TALENscomprising a FokI DNA cleavage domain, a target site typically comprisesa left half-site (bound by one monomer of the nuclease), a righthalf-site (bound by the second monomer of the nuclease), and a spacersequence between the half sites in which the cut is made. This structure([left half-site]-[spacer sequence]-[right half-site]) is referred toherein as an LSR structure. In some embodiments, the left half-siteand/or the right half-site is between 10-18 nucleotides long. In someembodiments, either or both half-sites are shorter or longer. In someembodiments, the left and right half sites comprise different nucleicacid sequences.

The term “Transcriptional Activator-Like Effector,” (TALE) as usedherein, refers to DNA binding proteins comprising a TALE repeat arrayand an effector domain. Typically, the TALE repeat array comprises aplurality of highly conserved 33-34 amino acid sequence comprising ahighly variable two-amino acid motif (Repeat Variable Diresidue, RVD).The RVD motif determines binding specificity to a nucleic acid sequence,and can be engineered according to methods well known to those of skillin the art to specifically bind a desired DNA sequence (see, e.g.,Miller, Jeffrey; et. al. (February 2011). “A TALE nuclease architecturefor efficient genome editing”. Nature Biotechnology 29 (2): 143-8;Zhang, Feng; et. al. (February 2011). “Efficient construction ofsequence-specific TAL effectors for modulating mammalian transcription”.Nature Biotechnology 29 (2): 149-53; Geiβler, R.; Scholze, H.; Hahn, S.;Streubel, J.; Bonas, U.; Behrens, S. E.; Boch, J. (2011), Shiu,Shin-Han. ed. “Transcriptional Activators of Human Genes withProgrammable DNA-Specificity”. PLoS ONE 6 (5): e19509; Boch, Jens(February 2011). “TALEs of genome targeting”. Nature Biotechnology 29(2): 135-6; Boch, Jens; et. al. (December 2009). “Breaking the Code ofDNA Binding Specificity of TAL-Type III Effectors”. Science 326 (5959):1509-12; and Moscou, Matthew J.; Adam J. Bogdanove (December 2009). “ASimple Cipher Governs DNA Recognition by TAL Effectors”. Science 326(5959): 1501; the entire contents of each of which are incorporatedherein by reference). The simple relationship between amino acidsequence and DNA recognition has allowed for the engineering of specificDNA binding domains by selecting a combination of repeat segmentscontaining the appropriate RVDs. As used herein in the context of TALEproteins, the term “effector” or “effector domain” refers to a molecule,moiety, or domain capable of modifying a nucleic acid and/or modulatingtranscription of one or more genes of a nucleic acid. In someembodiments, the effector domain comprises a nuclease, a recombinase, atranscriptional activator, a transcriptional repressor, or an epigenomemodifying enzyme or domain (e.g., a methyltransferase, demethylase,acetyltransferase, acetylase, etc.). Exemplary effectors are providedherein and additional suitable effectors will be apparent to those ofskill in the art. The disclosure is not limited in this respect.

The term “Transcriptional Activator-Like Element Nuclease,” (TALEN) asused herein, refers to an artificial nuclease comprising atranscriptional activator like effector DNA binding domain to a DNAcleavage domain, for example, a FokI domain. A number of modularassembly schemes for generating engineered TALE constructs have beenreported (Zhang, Feng; et. al. (February 2011). “Efficient constructionof sequence-specific TAL effectors for modulating mammaliantranscription”. Nature Biotechnology 29 (2): 149-53; Geipler, R.;Scholze, H.; Hahn, S.; Streubel, J.; Bonas, U.; Behrens, S. E.; Boch, J.(2011), Shiu, Shin-Han. ed. “Transcriptional Activators of Human Geneswith Programmable DNA-Specificity”. PLoS ONE 6 (5): e19509; Cermak, T.;Doyle, E. L.; Christian, M.; Wang, L.; Zhang, Y.; Schmidt, C.; Baller,J. A.; Somia, N. V. et al. (2011). “Efficient design and assembly ofcustom TALEN and other TAL effector-based constructs for DNA targeting”.Nucleic Acids Research; Morbitzer, R.; Elsaesser, J.; Hausner, J.;Lahaye, T. (2011). “Assembly of custom TALE-type DNA binding domains bymodular cloning”. Nucleic Acids Research; Li, T.; Huang, S.; Zhao, X.;Wright, D. A.; Carpenter, S.; Spalding, M. H.; Weeks, D. P.; Yang, B.(2011). “Modularly assembled designer TAL effector nucleases fortargeted gene knockout and gene replacement in eukaryotes”. NucleicAcids Research.; Weber, E.; Gruetzner, R.; Werner, S.; Engler, C.;Marillonnet, S. (2011). Bendahmane, Mohammed. ed. “Assembly of DesignerTAL Effectors by Golden Gate Cloning”. PLoS ONE 6 (5): e19722; theentire contents of each of which are incorporated herein by reference).

The terms “treatment,” “treat,” and “treating,” refer to a clinicalintervention aimed to reverse, alleviate, delay the onset of, or inhibitthe progress of a disease or disorder, or one or more symptoms thereof,as described herein. As used herein, the terms “treatment,” “treat,” and“treating” refer to a clinical intervention aimed to reverse, alleviate,delay the onset of, or inhibit the progress of a disease or disorder, orone or more symptoms thereof, as described herein. In some embodiments,treatment may be administered after one or more symptoms have developedand/or after a disease has been diagnosed. In other embodiments,treatment may be administered in the absence of symptoms, e.g., toprevent or delay onset of a symptom or inhibit onset or progression of adisease. For example, treatment may be administered to a susceptibleindividual prior to the onset of symptoms (e.g., in light of a historyof symptoms and/or in light of genetic or other susceptibility factors).Treatment may also be continued after symptoms have resolved, forexample to prevent or delay their recurrence.

DETAILED DESCRIPTION

Modified TALE Domains and Proteins that Bind Non-Canonical 5′Nucleotides

Modified TALE N-Terminal Domains

Some aspects of this disclosure are based on the recognition thatcertain modifications (e.g., mutations or amino acid substitutions)within TALE proteins or TALE domains affect the target nucleic acidbinding specificity with respect to the 5′ nucleotide of a targetnucleic acid. Accordingly, some aspects of this disclosure provideproteins with modified TALE N-terminal domains. In some embodiments, thedisclosure provides proteins comprising an amino acid sequence that isat least 80% identical to the amino acid sequence of SEQ ID NO: 1 withan alanine to glutamic acid amino acid substitution at amino acidresidue 39 (A39E) and/or a lysine to glutamic acid amino acidsubstitution at amino acid residue 19 (K19E) as compared to (SEQ IDNO: 1) or a homologous residue in a canonical N-terminal TALE domain. Asused herein, a “a canonical N-terminal TALE domain,” refers to anynaturally occurring N-terminal TALE domain. In some embodiments, theN-terminal TALE domain is from a Xanthomonas bacteria. ExemplaryXanthomonas bacteria include, without limitation, X. campestris, X.euvesicatoria, X. citri, X. axonopodis, X. alfalfa, X. perforans, X.vesicatoria, X. smithii, and X. gardneri. N-terminal TALE domains areknown in the art and would be recognized by the skilled artisan. In someembodiments a canonical N-terminal TALE domain comprises the amino acidsequence of SEQ ID NO: 1. In some embodiments a canonical N-terminalTALE domain consists of the amino acid sequence of SEQ ID NO: 1. In someembodiments, a canonical N-terminal TALE domain consists essentially ofthe amino acid sequence of SEQ ID NO: 1. For the purpose of clarity,lysine 19 (K19) and alanine 39 (A39) of SEQ ID NO: 1 are underlined andin bold as shown below.

Canonical N-terminal TALE domain (SEQ ID NO: 1) VDLRTLGYSQQQQEKIKP KVRSTVAQHHEALVGHGFTH A HIVALSQHPAALGTVAVKYQDMIAALPEATHEAIVGVGKQWSGARALEALLTVAGELRGPPLQLDTGQLLKIAKRGGVTAVEAVHAWRNALTGAPLN

In some embodiments, the disclosure provides proteins comprising anamino acid sequence that is at least 80% identical to the amino acidsequence of SEQ ID NO: 1 with an alanine to glutamic acid amino acidsubstitution at amino acid residue 39 (A39E) and/or a lysine to glutamicacid amino acid substitution at amino acid residue 19 (K19E) as comparedto a homologous residue in a canonical N-terminal TALE domain. Theconcept of homology and a “homologous residue” is known in the art andwould be recognized by a skilled artisan. Further, exemplary computersoftware used to determine homology between two sequences include, butare not limited to, GCG program package, Devereux, J., et al., NucleicAcids Research, 12(1), 387 (1984)), BLASTP, BLASTN, and FASTA Atschul,S. F. et al., J. Molec. Biol., 215, 403 (1990)). It should beappreciated that when the amino acid residues of SEQ ID NO: 1 (e.g.,amino acid residues K19 and A30 of SEQ ID NO: 1) are being compared tothe amino acid residues of a canonical N-terminal TALE domain, the aminoacid sequences may not be the same length and thus, the numbering schemebetween SEQ ID NO: 1 and the canonical N-terminal TALE domain may notalign with respect to homologous amino acid residues. Accordingly, theamino acid substitutions provided herein may be identified as comparedto a homologous residue in a canonical N-terminal TALE domain ratherthan by an absolute amino acid position within an amino acid sequence.

In some embodiments, the proteins of the present disclosure comprise anamino acid sequence that is at least 80% identical to the amino acidsequence of SEQ ID NO: 1 with an alanine to glutamic acid amino acidsubstitution at amino acid residue 39 (A39E) as compared to (SEQ IDNO: 1) or a homologous residue in a canonical N-terminal TALE domain. Insome embodiments, the proteins of the present disclosure comprise anamino acid sequence that is at least 80% identical to the amino acidsequence of SEQ ID NO: 1 with a lysine to glutamic acid amino acidsubstitution at amino acid residue 19 (K19E) as compared to (SEQ IDNO: 1) or a homologous residue in a canonical N-terminal TALE domain. Insome embodiments, the proteins of the present disclosure comprise anamino acid sequence that is at least 80% identical to the amino acidsequence of SEQ ID NO: 1 with an alanine to glutamic acid amino acidsubstitution at amino acid residue 39 (A39E) and a lysine to glutamicacid amino acid substitution at amino acid residue 19 (K19E) as comparedto (SEQ ID NO: 1) or a homologous residue in a canonical N-terminal TALEdomain.

In some embodiments, the proteins of the present disclosure comprise anamino acid sequence that is at least 82% identical, at least 84%identical, at least 86% identical, at least 88% identical, at least 90%identical, at least 92% identical, at least 94% identical, at least 95%identical, at least 96% identical, at least 97% identical, at least 98%identical, or at least 99% identical to SEQ ID NO: 1. In someembodiments, the proteins of the present disclosure comprise an alanineto glutamic acid substitution at amino acid residue 93 (A93E) ascompared to SEQ ID NO: 1 or a homologous residue in a canonicalN-terminal TALE domain. In some embodiments, the proteins of the presentdisclosure comprise a glycine to arginine amino acid substitution atamino acid residue 98 (G98R) as compared to SEQ ID NO: 1 or a homologousresidue in a canonical N-terminal TALE domain. In some embodiments, theproteins of the present disclosure comprise one or more of amino acidsubstitution S22N, G77D, A85T, T91A, A93G, P99S, P99T, A129E, and N136Tas compared to SEQ ID NO: 1, or a homologous residue in a canonicalN-terminal TALE domain. In some embodiments, the proteins of the presentdisclosure comprise an arginine to tryptophan amino acid substitution atamino acid residue 21 (R21W) as compared to SEQ ID NO: 1 or a homologousresidue in a canonical N-terminal TALE domain. In some embodiments, theproteins of the present disclosure may comprise one or more of aminoacid substitutions K19E, S22N, A39E, G77D, A85T, T91A, A93E, A93G, G98R,P99S, P99T, A129E, and N136T as compared to SEQ ID NO: 1, or ahomologous residue in a canonical N-terminal TALE domain.

Modified TALE Repeat Arrays

Some aspects of this disclosure are based on the recognition thatcertain modifications (e.g., mutations or amino acid substitutions)within a TALE repeat array alter the target nucleic acid bindingspecificity with respect to the 5′ nucleotide of a target nucleic acid.Aspects of the disclosure provide proteins comprising one or more TALErepeat sequences, which may be combined (e.g., in tandem) to form TALErepeat arrays. TALE repeat arrays are typically made up of multiple34-amino acid TALE repeat sequences, each of which uses arepeat-variable di-residue (RVD), typically the amino acids at positions12 and 13, to recognize a target site. TALE repeat sequences are knownin the art and have been described previously, for example, in Tebas, P.et al. Gene editing of CCR5 in autologous CD4 T cells of personsinfected with HIV. N Engl J Med 370, 901-10 (2014) and Genovese, P. etal. Targeted genome editing in human repopulating haematopoietic stemcells. Nature 510, 235-40 (2014), the contents of each of which areincorporated herein by reference. Examples of RVDs that enablerecognition of each of the four DNA base pairs are known, enablingarrays of TALE repeats to be constructed that can bind virtually any DNAsequence. As used herein, a “TALE repeat sequence” refers to an aminoacid sequence that is at least 80% identical to the amino acid sequenceof SEQ ID NO: 2, including any of the amino acid substitutions disclosedherein.

Accordingly, aspects of the disclosure relate to proteins comprising anamino acid sequence that is at least 80% identical to the amino acidsequence of SEQ ID NO: 2. The letter “X” in SEQ ID NO: 2 specifies anyamino acid residue and the subscript numbers immediately right of the“X” are used to identify each “X” in the amino acid sequence for thepurpose of clarity. In some embodiments, amino acid positions 12 and 13of SEQ ID NO: 2, specified by X₃ and X₄ respectively, therepeat-variable di-residue (RVD). For the purpose of clarity, residues12 and 13, of SEQ ID NO: 2 are underlined and in bold as shown below.

General formula of a TALE repeat sequence:

(SEQ ID NO: 2) LTPX₁QVVAIAX₂ X ₃ X ₄GGX₅X₆ALETVQRLLPVLCQX₇HG.In some embodiments, X₁ is D, E or A, X₂ is S or N, X₃ is N or H, X₄ isG, D, I, or N, X₅ is K or R, X₆ is Q or P, and/or X₇ is D or A as shownin SEQ ID NO: 2. In some embodiments, the proteins of the presentdisclosure comprise one or more of the following amino acidsubstitutions: T2A, P3L, P3S, X₁4G, X₁4K, X₁4N, X₂11K, X₂11Y, X₃12H,X₄13K, X₄13H, G15S, X₅16R, X₆17P, T21A, L26F, P27S, V28G, Q31K, X₇32S,D32E, and H33L as compared to SEQ ID NO: 2. In some embodiments, theproteins of the present disclosure comprise an amino acid sequence is atleast 82% identical, at least 84% identical, at least 86% identical, atleast 88% identical, at least 90% identical, at least 92% identical, atleast 94% identical, at least 95% identical, at least 96% identical, atleast 97% identical, at least 98% identical, or at least 99% identicalto SEQ ID NO: 2.

In some embodiments, the proteins of the present disclosure comprise oneor more of the following amino acid substitutions: P3L, X₁4G, X₁4K,X₂11Y, X₅16R, X₆17P, T21A, and L26F as compared to SEQ ID NO: 2. In someembodiments, the proteins of the present disclosure comprise one or moreof the following amino acid substitutions: P3S, X₁4K, X₃12H, X₅16R, andL26F as compared to SEQ ID NO: 2. In some embodiments, the proteins ofthe present disclosure comprise one or more of the following amino acidsubstitutions: X₁4N, X₁4K, X₂11K, G15S, X₅16R, L26F, P27S, A32S, D32E,and H33L as compared to SEQ ID NO: 2. In some embodiments, the proteinsof the present disclosure comprise one or more of the following aminoacid substitutions: T2A, P3L, X₁4K, X₃12H, V28G, and Q31K as compared toSEQ ID NO: 2. In some embodiments, the proteins of the presentdisclosure comprise one or more of the following amino acidsubstitutions: X₁4N, X₁4K, X₂11K, X₅16R, T21A, and L26F as compared toSEQ ID NO: 2. In some embodiments, the proteins of the presentdisclosure comprise one or more of the following amino acidsubstitutions: A8G, X₄13K, X₄13H, A18G, E20G, Q23K, L26A, H33P, H33Y,and G34S as compared to SEQ ID NO: 2.

In some embodiments, the proteins of the present disclosure comprise aplurality of TALE repeat sequences that are at least 82% identical, atleast 84% identical, at least 86% identical, at least 88% identical, atleast 90% identical, at least 92% identical, at least 94% identical, atleast 95% identical, at least 96% identical, at least 97% identical, atleast 98% identical, or at least 99% identical to SEQ ID NO: 2. In someembodiments, the proteins of the present disclosure comprise a pluralityof TALE repeat sequences that are made up of at least 2, at least 3, atleast 4, at least 5, at least 6, at least 7, at least 8, at least 9, atleast 10, at least 11, at least 12, at least 13, at least 14, at least15, at least 16, at least 17, at least 18, at least 19, at least 20, atleast 25, at least 30, at least 40, at least 50, at least 60, at least80, or at least 100 of the TALE repeat sequences disclosed herein.

The plurality of TALE repeat sequences of the present disclosure may bearranged in any order. In some embodiments, the proteins provided hereinhave one or more TALE repeat sequences that are directly adjoined(contiguous) to each other without a linker. For example the C-terminalamino acid residue of a first TALE repeat sequence may be directlyadjoined to the N-terminal amino acid residue (e.g., by a peptide bond)to generate a protein having a plurality of TALE repeat sequences thatare directly adjoined. In some embodiments, the TALE repeat sequencesare not directly adjoined. For example, the TALE repeat sequences may bejoined by one or more linkers. In some embodiments the one or morelinkers comprises an amino acid linker. In some embodiments, the one ormore amino acid linkers is at least 1 amino acid, at least 2 aminoacids, at least 3 amino acids, at least 4 amino acids, at least 5 aminoacids, at least 6 amino acids, at least 7 amino acids, at least 8 aminoacids, at least 9 amino acids, at least 10 amino acids, at least 15amino acid, at least 20 amino acids, at least 25 amino acids, at least30 amino acids, at least 40 amino acids, at least 50 amino acids, atleast 60 amino acids, at least 80 amino acids, or at least 100 aminoacids in length. It should be appreciated that the proteins, describedherein, may comprise both TALE repeat sequences that are directlyadjoined as well as TALE repeat sequences that are joined by one or morelinkers.

In some embodiments, the plurality of TALE repeat sequences form a TALErepeat array. As used herein, a “TALE repeat array” refers to at least 5TALE repeat sequences that are directly adjoined. In some embodiments,the TALE repeat array comprises at least 4, at least 5, at least 6, atleast 7, at least 8, at least 9, at least 10, at least 11, at least 12,at least 13, at least 14, at least 15, at least 16, at least 17, atleast 18, at least 19, at least 20, at least 25, at least 30, at least35, at least 40, at least 45, at least 50, at least 55, at least 60, atleast 65, at least 70, at least 75, at least 80, at least 85, at least90, at least 95, or at least 100 TALE repeat sequences. In someembodiments, the TALE repeat array comprises at least 6, at least 7, atleast 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,25, 26, 27, 28, 29, or 30 TALE repeat sequences, either used alone or incombination with other TALE arrays. In some embodiments, the proteins ofthe present disclosure comprise an amino acid sequence is at least 80%identical to the amino acid sequence provided in SEQ ID NO: 6. In someembodiments, the proteins of the present disclosure comprise one or moreof the following amino acid substitutions: K16R; K50R; L94F; T104A;P173L; L196F; K220R; L230F; A236S; N249Y; Q255P; T259A; D276G; L332F;Q337K; H373L; P377L; N386H; G389S; P401S; D406E; P411S; D412N; V436G;E446K; N453K; N455K; K458R; and P513L; as compared to SEQ ID NO:6. ortheir corresponding equivalent substitutions in similar TALEs)

In some embodiments, the proteins of the present disclosure comprise anamino acid sequence is at least 82% identical, at least 84% identical,at least 86% identical, at least 88% identical, at least 90% identical,at least 92% identical, at least 94% identical, at least 95% identical,at least 96% identical, at least 97% identical, at least 98% identical,or at least 99% identical to SEQ ID NO: 6. In some embodiments, theproteins of the present disclosure comprise a TALE repeat arraycomprising an amino acid substitution or a combination of amino acidsubstitutions selected from the following: K50R and L230F; L230F; L230Fand N249Y; Q255P; T259A; P377L; and D276G, E446K, and P513L; as comparedto SEQ ID NO: 6. In some embodiments, the proteins of the presentdisclosure comprise a TALE repeat array comprising one of the amino acidsubstitutions or combination of amino acid substitutions selected from:K50R and N453K; L332F and K458R; N386H; P411S and N453K; E446K; N453K;and K458R; as compared to SEQ ID NO: 6. In some embodiments, theproteins of the present disclosure comprise a TALE repeat arraycomprising one of the amino acid substitutions or combination of aminoacid substitutions selected from: K16R, G389S, and E446K; K16R, G389S,and E446K; L94F; L196F, G389S, P401S, and E446K; K220R; A236S, G389S,and E446K; H373L and D412N; G389S, D406E, and E446K; D412N; and N455K;as compared to SEQ ID NO: 6. In some embodiments, the proteins of thepresent disclosure comprise a TALE repeat array comprising one of theamino acid substitutions or combination of amino acid substitutionsselected from: T104A, Q337K, N386H, and E446K; P173L, Q337K, N386H,E446K, and V436G; and Q337K, N386H, E446K, and V436G; as compared to SEQID NO: 6.

Modified TALE C-Terminal Domains

Some aspects of this disclosure are based on the recognition thatcertain modifications (e.g., truncations, mutations or amino acidsubstitutions) of a TALE C-terminal domain affect the target nucleicacid binding specificity with respect to the 5′ nucleotide of a targetnucleic acid. In some embodiments, the disclosure provides proteinscomprising an amino acid sequence that is at least 80% identical to theamino acid sequence of any one of SEQ ID NOs: 3, 4, or 5 with aglutamine to proline amino acid substitution at amino acid residue 5(Q5P) as compared to either SEQ ID NO: 3, 4, or 5, or a homologousresidue in a canonical C-terminal TALE domain. As used herein, a “acanonical C-terminal TALE domain,” refers to any naturally occurringC-terminal TALE domain. In some embodiments, the C-terminal TALE domainis from a Xanthomonas bacteria. Exemplary Xanthomonas bacteria include,without limitation, X. campestris, X. euvesicatoria, X. citri, X.axonopodis, X. alfalfa, X. perforans, X. vesicatoria, X. smithii, and X.gardneri. C-terminal TALE domains are known in the art and would berecognized by the skilled artisan. In some embodiments a canonicalC-terminal TALE domain comprises any one of the amino acid sequences ofSEQ ID NOs: 3, 4, or 5. In some embodiments, a canonical C-terminal TALEdomain consists of any one of the amino acid sequences of SEQ ID NOs: 3,4, or 5. In some embodiments, a canonical C-terminal TALE domainconsists essentially of any one of the amino acid sequences of SEQ IDNOs: 3, 4, or 5. As used herein, a “C-terminal TALE domain” or“C-terminal domain” refers to any of the canonical C-terminal TALEdomains or any of the modified TALE C-terminal domains provided herein.

In some embodiments, the proteins of the present disclosure comprise anamino acid sequence that is at least 82% identical, at least 84%identical, at least 86% identical, at least 88% identical, at least 90%identical, at least 92% identical, at least 94% identical, at least 95%identical, at least 96% identical, at least 97% identical, at least 98%identical, or at least 99% identical to any one of SEQ ID NOs: 3, 4, or5.

Modified TALE Proteins

Some aspects of this disclosure are based on the surprising discoverythat certain modifications (e.g., truncations, mutations and/or aminoacid substitutions) of TALE proteins affect the target nucleic acidbinding specificity with respect to the 5′ nucleotide of a targetnucleic acid. Typically, a TALE protein, comprises the followingstructure:

-   -   [N-terminal domain]-[TALE repeat array]-[C-terminal domain]        where each“−” individually indicates conjugation, either        covalently or non-covalently, and where the conjugation can be        direct, e.g., via direct bond, or indirect, e.g., via a linker.

In some embodiments, the N-terminal domain comprises any of the modifiedTALE N-terminal domains provided herein. In some embodiments, the TALErepeat array comprises any of the modified TALE repeat arrays providedherein. In some embodiments, the C-terminal domain comprises any of themodified TALE C-terminal domains provided herein. In some embodiments,the N-terminal domain comprises a truncated version of the N-terminaldomain. In some embodiments, the C-terminal domain comprises a truncatedversion of the C-terminal domain. In some embodiments, the truncateddomain comprises less than 90%, less than 80%, less than 70%, less than60%, less than 50%, less than 40%, less than 30%, or less than 25% ofthe residues of the canonical domain. In some embodiments, the truncatedC-terminal domain comprises less than 60, less than 50, less than 40,less than 30, less than 29, less than 28, less than 27, less than 26,less than 25, less than 24, less than 23, less than 22, less than 21, orless than 20 amino acid residues. In some embodiments, the truncatedC-terminal domain comprises 60, 59, 58, 57, 56, 55, 54, 53, 52, 51, 50,49, 48, 47, 46, 45, 44, 43, 42, 41, 40, 39, 38, 37, 36, 35, 34, 33, 32,31, 30, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24,23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, or 10 residues. Insome embodiments, the N-terminal domain and the TALE repeat array aredirectly adjoined. In some embodiments, the N-terminal domain and theTALE repeat array are joined by a linker. In some embodiments, the TALErepeat array and the C-terminal domain are directly adjoined. In someembodiments, the TALE repeat array and the C-terminal domain are joinedby a linker.

In some embodiments, the protein further comprises an effector domain.In some embodiments, the effector domain may be positioned N-terminal orC-terminal to an N-terminal domain, a TALE repeat array, or a C-terminaldomain of the protein. In some embodiments, the protein comprises thestructure [N-terminal domain]-[TALE repeat array]-[C-terminaldomain]-[effector domain], or [effector domain]-[N-terminaldomain]-[TALE repeat array]-[C-terminal domain].

In some embodiments, the effector domain comprises a nuclease domain, atranscriptional activator or repressor domain, a recombinase domain, oran epigenetic modification enzyme domain. The effector domains providedherein can be used in the context of suitable TALE effector molecules,e.g., TALE nucleases, TALE transcriptional activators, TALEtranscriptional repressors, TALE recombinases, and TALE epigenomemodification enzymes. Additional suitable TALE effectors in the contextof which the isolated TALE domains can be used will be apparent to thoseof skill in the art based on this disclosure. In general, the TALEproteins provided herein are engineered to bind a target sequence with anon-canonical 5′ nucleotide (A, C, or G) over the native 5′ T, therebyexpanding the scope of DNA target sequences that can be bound a TALEprotein.

In some embodiments, the nuclease domain is monomeric. In someembodiments, the nuclease domain dimerizes or multimerizes in order tocleave a nucleic acid. Homo- or heterodimerization or multimerization ofTALEN monomers typically occurs via binding of the monomers to bindingsequences that are in sufficiently close proximity to allowdimerization, e.g., to sequences that are proximal to each other on thesame nucleic acid molecule (e.g., the same double-stranded nucleic acidmolecule). In some embodiments, the nuclease domain comprises a FokInuclease domain. In some embodiments, the FokI nuclease domain comprisesa homodimeric FokI domain. In some embodiments, the FokI nuclease domaincomprises a heterodimeric FokI domain. In some embodiments, the FokInuclease domain comprises the amino acid sequence of SEQ ID NO: 14. Insome embodiments, the FokI nuclease domain comprises the amino acidsequence that is at least 80% identical to the amino acid sequence ofSEQ ID NO: 14. It should be understood that the FokI sequences providedherein are exemplary and provided for the purpose of illustrating someembodiments embraced by the present disclosure. They are not meant to belimiting and additional FokI sequences useful according to aspects ofthis disclosure will be apparent to the skilled artisan based on thisdisclosure.

In some embodiments, the effector domain comprises a domain capable ofincreasing transcription of a gene. In some embodiments, the effectordomain comprises a transcriptional activation domain. As used herein, a“transcriptional activation” (TAD) refers to a region of a transcriptionfactor which in conjunction with a DNA binding domain can activatetranscription (e.g., from a promoter) by contacting transcriptionalmachinery (e.g., general transcription factors and RNA polymerase)either directly or through other proteins known as co-activators. Insome embodiments, the transcriptional activation domain is from anaturally-occurring transcriptional activator or is a protein homologousto a transcriptional activation domain from a naturally-occurringtranscriptional activator. Transcriptional activation domains are knownin the art and would be recognized by the skilled artisan. In someembodiments, the transcriptional activation domain is from a naturallyoccurring transcription factor. In some embodiments, the transcriptionfactor comprises a eukaryotic transcription factor. Exemplary eukaryotictranscription factors include, without limitation, p53, VP16, MLL, E2A,HSF1, NF-IL6, NFAT1 and NF-κB. In some embodiments, the transcriptionfactor comprises a prokaryotic transcription factor. In someembodiments, the prokaryotic transcription factor comprises a sigmafactor. Exemplary prokaryotic sigma factors include, without limitation,RpoD, FecI, RpoE, RpoF, RpoH, RpoS, and RpoN. In some embodiments, thetranscriptional activation domain comprises a domain from an RNApolymerase. In some embodiments, the transcriptional activation domaincomprises an omega subunit from RNA polymerase (RNAPω). In someembodiments, the RNA polymerase domain comprises an amino acid sequencethat is at least 80% identical to the amino acid sequence provided inSEQ ID NO: 10.

In some embodiments, the RNA polymerase domain comprises an amino acidsequence is at least 85% identical, at least 90% identical, at least 95%identical, at least 98% identical, at least 99% identical, or at least100% identical to the amino acid sequence provided in SEQ ID NO: 10. Insome embodiments, the RNA polymerase domain comprises one or more of thefollowing amino acid substitutions: V9G, D17G, M29T, P36S, and V38G ascompared to SEQ ID NO: 10, or a homologous canonical RNA polymerasedomain.

In some embodiments, the transcriptional activation domain comprises adomain from a transcription factor, e.g., a transactivating domain (TAD)regulating transcription. Suitable transactivating domains include,without limitation, those present in Gal4, Pdr1, Oaf1, GCN4, VP16, Pho4,Msn2, Ino2, and P201. In some embodiments, the transactivating domain isa transactivating domain of p53 (e.g., p53TAD1, p53TAD2), MLL, E2A,Rtg3, CREB, CREBb6a, Gli3, Gal4, Pip1, or Pip3, e.g., a 9aa TAD of anyof these proteins. In addition, small RNA sequences capable of directlysupporting transcription which could be fused to or covalently linkeddirectly or through a secondary scaffold to the evolved DBD are embracedby this disclosure.

In some embodiments, the effector domain comprises a domain capable ofdecreasing transcription of a gene. In some embodiments, the effectordomain comprises a transcriptional repressor domain. As used herein, a“transcriptional repressor domain” (TRD) refers to a region of atranscription factor which, in conjunction with a DNA binding domain,can repress transcription (e.g., from a promoter) by contactingtranscriptional machinery (e.g., general transcription factors and RNApolymerase) either directly or through other proteins known asco-repressors. Transcriptional repressor domains are known in the artand would be recognized by a skilled artisan. Transcriptional repressordomains, in the context of TALE DNA-binding proteins have been describedpreviously in Cong, L., Zhou, R., Kuo, Y. C., Cunniff, M. & Zhang, F.Comprehensive interrogation of natural TALE DNA-binding modules andtranscriptional repressor domains. Nat Commun 3, 968 (2012), thecontents of which are incorporated herein by reference. It should beappreciated that the transcriptional repressor domains described hereinand in the cited references are exemplary and are not meant to belimiting.

In some embodiments, the proteins of the present disclosure furthercomprise a linker, an epitope tag and/or a nuclear localization sequence(NLS). It will be apparent to those skilled in the art that it isdesirable in some embodiments to adjust the length of the linker whenlinking any of the proteins or protein domains (e.g., N-terminaldomains, TALE repeat sequences, TALE arrays, C-terminal domains, oreffector domains) described herein. For example, the length of thelinker may be used to accommodate truncated domains, e.g., truncatedC-terminal domains, or to optimally position an effector domain (e.g. anuclease domain, a transcriptional repressor domain, a transcriptionalactivator domain, a recombinase domain, or an epigenetic modificationenzyme domain) to perform a function (e.g. DNA cleaving, regulating, ormodifying a target sequence). In some embodiments, the linker comprisesan amino acid. In some embodiments, the linker comprises or consists ofone or more amino acids. In some embodiments, the amino acid linker isat least 1, at least 2, at least 3, at least 4, at least 5, at least 10,at least 20, at least 30, at least 40, at least 50, or at least 100amino acids in length. In some embodiments, the linker comprises theamino acid sequence provided in SEQ ID NO: 8. The linker may bepositioned between any of the proteins or protein domains, describedherein. In some embodiments, the linker is positioned between theC-terminal domain and the effector domain. In some embodiments, thelinker is positioned between the C-terminal domain and the effectordomain. In some embodiments, the linker is positioned between the TALErepeat array and the C-terminal domain. In some embodiments, the linkeris positioned between the N-terminal domain and the TALE repeat array.

In some embodiments, the proteins of the present disclosure comprise anepitope tag. An “epitope tag” as used herein refers to a peptidesequence that can be attached to a protein (e.g. by using molecularbiology techniques). Typically, epitope tags are short peptide sequencesthat high-affinity antibodies can bind (e.g., for the purposes ofdetection or affinity purification). Exemplary epitope tags include, butare not limited to V5-tag, Myc-tag, HA-tag and FLAG tag. In someembodiments, the epitope tag comprises a FLAG tag. In some embodiments,the FLAG tag comprises the amino sequence provided in SEQ ID NO: 63(DYKDDDDK).

In some embodiments, the proteins of the present disclosure comprise anuclear localization signal (NLS). A “nuclear localization signal” (NLS)as used herein, refers to a peptide sequence that targets a protein, towhich it is attached, to the nucleus. Typically, a NLS comprises one ormore short sequences of positively charged lysines or arginines exposedon the protein surface. Nuclear localization sequences are known in theart and would be apparent to a skilled artisan. NLSs have been describedpreviously, for example, in Kalderon D. et al., (1984). “A short aminoacid sequence able to specify nuclear location”. Cell 39 (3 Pt 2):499-509, and Dingwall C, Robbins J, Dilworth S M, Roberts B, RichardsonW D (September 1988). “The nucleoplasmin nuclear location sequence islarger and more complex than that of SV-40 large T antigen”. J CellBiol. 107 (3): 841-9, the contents of each of which are incorporatedherein by reference. In some embodiments, the NLS comprises the aminoacid sequence provided in SEQ ID NO: 64(PKKKRKV).

In some embodiments, the protein comprises an amino acid sequence thatis at least 80% identical to the amino acid sequence provided in SEQ IDNO: 9. In some embodiments, the protein further comprises an amino acidsequence that is at least 85% identical, at least 90% identical, atleast 95% identical, at least 98% identical, or at least 99% identicalto the amino acid sequence provided in SEQ ID NO: 9.

The epitope tag and/or the NLS may be positioned in any suitablelocation within any of the proteins described herein. In someembodiments, the epitope tag and/or the NLS is positioned N-terminal toan N-terminal domain, a TALE array, a C-terminal domain or an effectordomain. In some embodiments, the epitope tag and/or the NLS ispositioned C-terminal to an N-terminal domain, a TALE array, aC-terminal domain or an effector domain.

Numerous exemplary engineered TALE sequences have been provided herein.It will be understood that the present disclosure embraces all possiblecombinations of the various engineered TALE sequences, e.g.,combinations of any N-terminal TALE domain, any TALE repeat, and anyC-terminal TALE domain as provided herein. Those of skill in the artwill understand that the TALE repeat array will vary depending on thenucleic acid sequence to be targeted. Methods and strategies to tailor aTALE repeat array for a specific target sequence are well known to thoseof skill in the art. The disclosure embraces TALE repeat arraystargeting any suitable nucleic acid sequence and comprising either theTALE repeat array modifications disclosed herein or fused to anengineered TALE domain as provided herein. It will be understood bythose of skill in the art that the exemplary sequences provided hereinare for illustration purposes only and are not intended to limit thescope of the present disclosure. The disclosure also embraces the use ofeach of the inventive TALE proteins and TALE domains, e.g., the modifiedN-terminal domains, C-terminal domains, TALE arrays and RNAPω domainsdescribed herein. Additional sequences that are useful in accordance toaspects of this disclosure will be apparent to the skilled artisan.

Some TALE proteins disclosed herein are provided as a monomer. Some TALEproteins described herein comprise a nuclease domain (e.g., a FokIdomain). In some embodiments, the nuclease domain may dimerize to cleavea nucleic acid sequence. In some embodiments, the proteins describedherein are TALENs. In some embodiments the TALENs provide herein form ahomodimer. In some embodiments the TALENs provide herein form aheterodimer.

Some aspects of this disclosure are based on the recognition thatcertain modifications (e.g., mutations or amino acid substitutions)within TALE proteins or TALE domains (N-terminal domain, TALE array orC-terminal domain) affect the target nucleic acid binding specificity ofthe TALE with respect to the 5′ nucleotide of a target nucleic acid.Typically, TALEs have been limited to the target nucleic acid sequencesthat they bind because the 5′ nucleotide of the target site to whichthey bind is specified to be thymine (T). TALE domains with alternative5′ nucleotide specificities are described herein and expand the scope ofDNA target sequences that can be bound by TALEs. Accordingly in someembodiments, the engineered TALE proteins provided herein bind a targetsequence comprising an adenine (A) a cytosine (C), or a guanine (G) atthe 5′ end of a target sequence. In some embodiments, the TALE proteinsprovided herein bind a target sequence comprising a thymine (T) at the5′ end of a target sequence. In some embodiments the TALE proteinsprovided herein bind a target sequence comprising an adenine (A) acytosine (C), or a guanine (G) at the 5′ end of a target sequence withgreater affinity as compared to the target sequence having a thymine (T)in place of the A, C or G at the 5′ end of a target sequence. In someembodiments the TALE proteins provided herein bind a target sequencecomprising an adenine (A) a cytosine (C), or a guanine (G) at the 5′ endof a target sequence with at least 5%, at least 10%, at least 15%, atleast 20%, at least 25%, at least 30%, at least 35%, at least 40%, atleast 45%, at least 50%, at least 55%, at least 60%, at least 65%, atleast 70%, at least 75%, at least 80%, at least 85%, at least 90%, atleast 95%, at least 10%, at least 150%, at least 200%, at least 250%, atleast 300%, at least 350%, at least 400%, at least 450%, or at least500% greater affinity as compared to the target sequence having athymine (T) in place of the A, C or G at the 5′ end of a targetsequence.

The affinity of the TALE protein to the target sequence may bedetermined by any suitable method known in the art. In some embodimentsthe affinity of the TALE protein to the target sequence is determined bymeasuring the binding affinity of the TALE protein to the targetsequence. In some embodiments the affinity of the TALE protein to thetarget sequence is determined by indirectly measuring the bindingaffinity. For example, the binding affinity may be measured using anindirect readout such as expression of a nucleotide sequence (e.g., agene), cleavage of a nucleotide sequence, or modification of anucleotide sequence that is responsive to binding of the TALE protein toa target sequence. As one non-limiting example, a TALE proteincomprising a transcriptional activator domain may induce transcriptionof a reporter gene (e.g., a fluorescent reporter gene) upon binding to atarget sequence. Expression of the fluorescent reporter gene can bemeasured (e.g., based on fluorescence intensity) to determine therelative binding affinity of the TALE to one target sequence as comparedto another target sequence.

In some embodiments, TALENs provided herein cleave their target siteswith high specificity. For example, in some embodiments an engineeredTALEN is provided that has been engineered to cleave a desired targetsite (e.g., within a genome) while binding and/or cleaving less than 1,less than 2, less than 3, less than 4, less than 5, less than 6, lessthan 7, less than 8, less than 9, less than 10, less than 20, or lessthan 50 off-target sites at a concentration effective for the nucleaseto cut its intended target site within a genome. In some embodiments, aTALEN is provided that has been engineered to cleave a desired uniquetarget site that has been selected to differ from any other site (e.g.,within a genome) by at least 3, at least 4, at least 5, at least 6, atleast 7, at least 8, at least 9, or at least 10 nucleotide residues. Insome embodiments, a TALEN is provided that has been engineered to cleavea desired target site (e.g., within a genome) while binding and/orcleaving less than 1, less than 2, less than 3, less than 4, less than5, less than 6, less than 7, less than 8, less than 9 or less than 10off-target sites at a concentration effective for the nuclease to cutits intended target site. In some embodiments, a TALEN is provided thathas been engineered to cleave a desired unique target site that has beenselected to differ from any other site within a genome by at least 3, atleast 4, at least 5, at least 6, at least 7, at least 8, at least 9, orat least 10 nucleotide residues.

In some embodiments, an engineered TALEN is provided that cleaves atarget sequence more efficiently than one or more off-target sequences(e.g., in a genome). In some embodiments, an engineered TALEN isprovided that cleaves a target sequence more efficiently by at least 0.1fold, by at least 0.2 fold, by at least 0.3 fold, by at least 0.4 fold,by at least 0.5 fold, by at least 0.6 fold, by at least 0.7 fold, by atleast 0.8 fold, by at least 0.9 fold, by at least 1 fold, by at least 2fold, by at least 3 fold, by at least 4 fold, by at least 5 fold, by atleast 6 fold, by at least 7 fold, by at least 8 fold, by at least 9fold, by at least 10 fold, by at least 20 fold, by at least 30 fold, byat least 40 fold, by at least 50 fold, by at least 60 fold, by at least70 fold, by at least 80 fold, by at least 90 fold, or by at least 100fold as compared to one or more off-target sites (e.g., within a genome)at a concentration effective for the TALEN to cut its intended targetsite.

In some embodiments, the proteins provided herein comprise a TALE repeatarray that binds a target sequence comprised in a genome. The term“genome”, as used herein, refers to the genetic material of an organism.In some embodiments, the genome includes both the genes and thenon-coding sequences of the genome. In some embodiments the genomecomprises DNA. In some embodiments the genome comprises RNA. In someembodiments the genome comprises a eukaryotic genome, a prokaryoticgenome, or a viral genome. In some embodiments, the genome comprisesnon-chromosomal genetic elements such as viruses, plasmids transposableelements. In some embodiments, the genome comprises genetic materialstored within organelles that contain their own nucleic acids (e.g.,mitochondria or chloroplasts).

In some embodiments, the genome is comprised in a cell. In someembodiments, the genome is comprised in a cell from an established cellline (e.g., a 293T cell), or a primary cell cultured ex vivo (e.g.,cells obtained from a subject and grown in culture). In someembodiments, the genome is comprised in a hematologic cell (e.g.,hematopoietic stem cell, leukocyte, or thrombocyte), or a cell from asolid tissue, such as a liver cell, a kidney cell, a lung cell, a heartcell, a bone cell, a skin cell, a brain cell, or any other cell found ina subject. In some embodiments, the genome or the cell comprising thegenome is in a subject. Subjects comprising the genomes of the presentdisclosure include, but are not limited to, humans and/or otherprimates; mammals, including, but not limited to, cattle, pigs, horses,sheep, cats, dogs, mice, and/or rats; and/or birds, includingcommercially relevant birds such as chickens, ducks, geese, and/orturkeys.

The target sequence of any of the TALEs provided herein may bind atarget sequence that is within a gene or in proximity to a gene known tobe associated with a disease or disorder. In some embodiments, TALEsprovided herein may be used for therapeutic purposes. For example, insome embodiments, TALEs provided herein may be used for treatment of anyof a variety of diseases, disorders, and/or conditions, including butnot limited to one or more of the following: autoimmune disorders (e.g.diabetes, lupus, multiple sclerosis, psoriasis, rheumatoid arthritis);inflammatory disorders (e.g. arthritis, pelvic inflammatory disease);infectious diseases (e.g. viral infections (e.g., HIV, HCV, RSV),bacterial infections, fungal infections, sepsis); neurological disorders(e.g. Alzheimer's disease, Huntington's disease; autism; Duchennemuscular dystrophy); cardiovascular disorders (e.g. atherosclerosis,hypercholesterolemia, thrombosis, clotting disorders, angiogenicdisorders such as macular degeneration); proliferative disorders (e.g.cancer, benign neoplasms); respiratory disorders (e.g. chronicobstructive pulmonary disease); digestive disorders (e.g. inflammatorybowel disease, ulcers); musculoskeletal disorders (e.g. fibromyalgia,arthritis); endocrine, metabolic, and nutritional disorders (e.g.diabetes, osteoporosis); urological disorders (e.g. renal disease);psychological disorders (e.g. depression, schizophrenia); skin disorders(e.g. wounds, eczema); blood and lymphatic disorders (e.g. anemia,hemophilia); etc. In some embodiments, the TALE comprises an effectordomain. For example, the effector domain may comprise a nuclease (e.g.,a FokI domain). In some embodiments, the TALE (e.g., a TALEN) cleavesthe target sequence upon dimerization of the nuclease domains when boundto the target sequence. In the context of TALENs, it should beappreciated that cleavage of a target site can occur upon dimerizationof any of the TALENs described herein when bound to a target sequence.In some embodiments, the TALE comprises a transcriptional activator orrepressor domain, a recombinase domain, or an epigenetic modificationenzyme domain.

In some embodiments, a TALE provided herein cleaves a target site withinan allele that is associated with a disease or disorder. In someembodiments, a TALE provided herein modulates expression of a geneassociated with a disease or disorder when bound to a target site withinthe gene or in proximity to the gene. In some embodiments, the TALEcleaves a target site the cleavage of which results in the treatment orprevention of a disease or disorder. In some embodiments, the TALE bindsa target site and modulates expression of a gene associated with adisease or disorder, which results in the treatment or prevention of thedisease or disorder. In some embodiments, the disease is HIV/AIDS. Insome embodiments, the disease is a proliferative disease. In someembodiments, the TALE binds a CCR5 target sequence (e.g., a CCR5sequence associated with HIV). In some embodiments, the TALE binds anATM target sequence (e.g., an ATM target sequence associated with ataxiatelangiectasia). In some embodiments, the TALE binds a VEGFA targetsequence (e.g., a VEGFA sequence associated with a proliferativedisease). In some embodiments, the TALE binds a CFTR target sequence(e.g., a CFTR sequence associated with cystic fibrosis). In someembodiments, the TALE binds a dystrophin target sequence (e.g., adystrophin gene sequence associated with Duchenne muscular dystrophy).In some embodiments, the TALE binds a CBX8 target sequence (e.g., a CBX8sequence associated with a proliferative disease). In some embodiments,the TALE binds a target sequence associated with haemochromatosis,haemophilia, Charcot-Marie-Tooth disease, neurofibromatosis,phenylketonuria, polycystic kidney disease, sickle-cell disease, orTay-Sachs disease. Suitable target genes, e.g., genes causing the listeddiseases, are known to those of skill in the art. Additional genes andgene sequences associated with a disease or disorder will be apparent tothose of skill in the art. Exemplary monogenic disease which can betargeted by the nucleases provided herein, and for which additional TALEor zinc finger nucleases could be evolved using the technology presentedherein, include, but are not limited to any of the monogenic diseaseslisted athealthxchange.com.sg/News/Pages/Genetic-link-to-4000-diseases.aspx,and/or at genecards.org/cgi-bin/listdiseasecards.pl, the entire contentsof each of which are incorporated herein by reference. In addition, insome embodiments, tractable polygenic diseases are embraced. The TALEsprovided herein may modulate (e.g., increase, decrease or prevent)transcription of a gene when the TALE is bound to the target sequence.It should be appreciated that the target sequence may be within the geneor in proximity to the gene. When a TALE is bound to a target sequencein proximity to a gene, the TALE may modulate expression of the gene byregulating (e.g., promoting, or inhibiting) transcription of the gene(e.g., by binding a target sequence at or near a promoter sequence).Accordingly, in some embodiments, the TALE binds to a target sequencethat is at least 1, at least 5, at least 10, at least 20, at least 50,at least 100, at least 200, at least 300, at least 400, at least 500, atleast 600, at least 700, at least 800, at least 900, or at least 1000nucleotides from the transcription start site of the gene to modulateexpression of the gene. In some embodiments, the TALE protein increasestranscription of the gene when the protein is bound to the targetsequence. In some embodiments the TALE protein increases transcriptionof the gene by at least 1%, by at least 2%, by at least 5%, by at least10%, by at least 15%, by at least 20%, by at least 25%, by at least 30%,by at least 35%, by at least 40%, by at least 45%, by at least 50%, byat least 60%, by at least 70%, by at least 80%, by at least 90%, by atleast 100%, by at least 150%, or by at least 200% when the protein isbound to the target sequence. In some embodiments, the TALE proteindecreases transcription of the gene when the protein is bound to thetarget sequence. In some embodiments the TALE protein decreasestranscription of the gene by at least 1%, by at least 2%, by at least5%, by at least 10%, by at least 15%, by at least 20%, by at least 25%,by at least 30%, by at least 35%, by at least 40%, by at least 45%, byat least 50%, by at least 60%, by at least 70%, by at least 80%, by atleast 90%, or by at least 100% when the protein is bound to the targetsequence.

In the context of nucleases that dimerize, for example, nucleasescomprising a FokI DNA cleavage domain (e.g., TALENs), a target sitetypically comprises a left half-site (bound by one monomer of thenuclease), a right half-site (bound by the second monomer of thenuclease), and a spacer sequence between the half sites in which the cutis made. This structure ([left half-site]-[spacer sequence]-[righthalf-site]) is referred to herein as an LSR structure. In someembodiments, the left half-site and/or the right half-site is between5-50 nucleotides long. In some embodiments, the left half-site and/orthe right half-site is 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50nucleotides long. In some embodiments, both the left half-site and theright half-site are the same length. In some embodiments, either or bothhalf-sites are shorter or longer. In some embodiments, the left andright half sites comprise different nucleic acid sequences. In someembodiments the target sequence comprises a left half-site. In someembodiments, the target sequence comprises a right half-site. In someembodiments, the target sequence comprises a left half-site and a righthalf-site. In some embodiments, the left half-site and/or the righthalf-site comprise an adenine (A), a cytosine (C), or a guanine (G) atthe 5′ position. In some embodiments, the left half-site and/or theright half-site comprise a thymine (T) at the 5′ position.

Compositions

Also within the scope of the disclosure are compositions comprising anyof the TALEs provided herein. In some embodiments, the compositioncomprises one or more of the TALEs provided herein. In some embodiments,the composition comprises the TALE nuclease (TALEN) monomer and adifferent TALE nuclease (TALEN) monomer that can form a heterodimer withthe TALEN, wherein the dimer exhibits nuclease activity.

In some embodiments, the TALE is provided in a composition formulatedfor administration to a subject, e.g., to a human subject. For example,in some embodiments, a pharmaceutical composition is provided thatcomprises the TALE and a pharmaceutically acceptable excipient. In someembodiments, the pharmaceutical composition is formulated foradministration to a subject. In some embodiments, the pharmaceuticalcomposition comprises an effective amount of the TALE for cleaving atarget sequence, for increasing transcription of a gene, for decreasingtranscription of a gene or for preventing transcription of a gene in acell in the subject. In some embodiments, the TALE binds a targetsequence within a gene known to be associated with a disease or disorderand wherein the composition comprises an effective amount of the TALENfor alleviating a symptom associated with the disease or disorder.

For example, some embodiments provide pharmaceutical compositionscomprising a TALE as provided herein, or a nucleic acid encoding such aTALE, and a pharmaceutically acceptable excipient. Pharmaceuticalcompositions may optionally comprise one or more additionaltherapeutically active substances.

Formulations of the pharmaceutical compositions described herein may beprepared by any method known or hereafter developed in the art ofpharmacology. In general, such preparatory methods include the step ofbringing the active ingredient into association with an excipient and/orone or more other accessory ingredients, and then, if necessary and/ordesirable, shaping and/or packaging the product into a desired single-or multi-dose unit.

Pharmaceutical formulations may additionally comprise a pharmaceuticallyacceptable excipient, which, as used herein, includes any and allsolvents, dispersion media, diluents, or other liquid vehicles,dispersion or suspension aids, surface active agents, isotonic agents,thickening or emulsifying agents, preservatives, solid binders,lubricants and the like, as suited to the particular dosage formdesired. Remington's The Science and Practice of Pharmacy, 21^(st)Edition, A. R. Gennaro (Lippincott, Williams & Wilkins, Baltimore, Md.,2006; incorporated herein by reference) discloses various excipientsused in formulating pharmaceutical compositions and known techniques forthe preparation thereof. Except insofar as any conventional excipientmedium is incompatible with a substance or its derivatives, such as byproducing any undesirable biological effect or otherwise interacting ina deleterious manner with any other component(s) of the pharmaceuticalcomposition, its use is contemplated to be within the scope of thisdisclosure.

In some embodiments, a composition provided herein is administered to asubject, for example, to a human subject, in order to effect a targetedgenomic modification within the subject. In some embodiments, cells areobtained from the subject and contacted with a nuclease or anuclease-encoding nucleic acid ex vivo, and re-administered to thesubject after the desired genomic modification has been effected ordetected in the cells. Although the descriptions of pharmaceuticalcompositions provided herein are principally directed to pharmaceuticalcompositions which are suitable for administration to humans, it will beunderstood by the skilled artisan that such compositions are generallysuitable for administration to animals of all sorts. Modification ofpharmaceutical compositions suitable for administration to humans inorder to render the compositions suitable for administration to variousanimals is well understood, and the ordinarily skilled veterinarypharmacologist can design and/or perform such modification with no morethan routine experimentation. Subjects to which administration of thepharmaceutical compositions is contemplated include, but are not limitedto, humans and/or other primates; mammals, including, but not limitedto, cattle, pigs, horses, sheep, cats, dogs, mice, and/or rats; and/orbirds, including commercially relevant birds such as chickens, ducks,geese, and/or turkeys.

In some embodiments, the TALEs, TALE domains, TALE-encoding or TALEdomain-encoding nucleic acids, compositions, and reagents describedherein are isolated. In some embodiments, the TALEs, TALE domains,TALE-encoding or TALE domain-encoding nucleic acids, compositions, andreagents described herein are purified, e.g., at least 60%, at least70%, at least 80%, at least 90%, or at least 95% pure.

Modified TALE Domains and Proteins that Specifically Target CBX8

In some embodiments, the protein comprises an amino acid sequence thatis at least 80% identical to the amino acid sequence provided in SEQ IDNO: 11, wherein the amino acid sequence comprises one of the amino acidsubstitutions or combination of amino acid substitutions selected from:A79E, P553L, and Q711P; A79E and L406F; A79E, L406F, and N425Y; A79E andQ711P; A79E, K226R, L406F, and Q711P; Q431P and Q711P; Q431P, Q711P, andP765S; T435A and Q711P; and D452G, E622K, and P689L; as compared to SEQID NO: 11.

In some embodiments, the protein comprises an amino acid sequence thatis at least 80% identical to the amino acid sequence provided in SEQ IDNO: 11, wherein the amino acid sequence comprises one of the amino acidsubstitutions or combination of amino acid substitutions selected from:A79E and N562H; A79E, L508F, and K634R; A79E, L508F, and K634R; G138Rand N629K; K226R and N629K; L508F and K634R; P587S and N629K; E622K; andK634R; as compared to SEQ ID NO: 11.

In some embodiments, the protein comprises an amino acid sequence thatis at least 80% identical to the amino acid sequence provided in SEQ IDNO: 11, wherein the amino acid sequence comprises one of the amino acidsubstitutions or combination of amino acid substitutions selected from:S62N, A125T, A412S, G565S, E622K, and V738G; A133G, H549L, D588N, andV738G; A133E, D588N, and V738G; A133G, D588N, and V738G; A133G, K396Rand N683K; A133E, H549L, D588N, and V738G; A133E, K396R, and N683K;G117D, A169E, G565S, D582E, E622K, and V738G; T131A, P139S, N176T,K192R, G565S, E622K and V738G; P139S, L372F, G565S, P577S, E622K, andV738G; P139T, L372F, G565S, P577S, E622K, and V738G; K192R, G565S,E622K, and V738G; L270F, N629K, and V738G; and N631K and V738G; ascompared to SEQ ID NO: 11.

In some embodiments, the protein comprises an amino acid sequence thatis at least 80% identical to the amino acid sequence provided in SEQ IDNO: 11, wherein the amino acid sequence comprises one of the amino acidsubstitutions or combination of amino acid substitutions selected from:K27N, K59E, Q513K, N562H, E622K, V612G, Q711P, M758T, and V767G; K27N,K59E, P349L, Q513K, N562H, E622K, V612G, Q711P, M758T, and V767G; K59E,T280A, Q513K, N562H, E622K, Q711P, D746G, and V767G; and K59E, R61W,T280A, Q513K, N562H, E622K, Q711P, D746G, and V767G; as compared to SEQID NO: 11.

In some embodiments, the protein comprises an amino acid sequence thatis at least 82% identical, at least 84% identical, at least 86%identical, at least 88% identical, at least 90% identical, at least 92%identical, at least 94% identical, at least 95% identical, at least 96%identical, at least 97% identical, at least 98% identical, or at least99% identical to the amino acid sequence provided in SEQ ID NO: 11comprising any of the amino acid substitutions or combination of aminoacid substitutions provided herein.

In the context of CBX8-targeting TALEs that dimerize, for example, TALEnucleases comprising a FokI DNA cleavage domain (e.g., TALENs), a CBX8target site typically comprises a left half-site (bound by one monomerof the nuclease), a right half-site (bound by the second monomer of thenuclease), and a spacer sequence between the half sites in which the cutis made. This structure ([left half-site]-[spacer sequence]-[righthalf-site]) is referred to herein as an LSR structure. In someembodiments, the left half-site comprises the nucleic acid sequence ofSEQ ID NOs: 15, 17, 19, 21, or 23. In some embodiments, the left halfsite comprises the nucleic acid sequence of SEQ ID NOs: 16, 18, 20, 22,or 24. In some embodiments, the left half-site or right half-sitecomprises any of the nucleic acid sequences below:

CBX8 on target sequence with 5′ T: (SEQ ID NO: 36)5′-TTCAGGAGGGCTTCGGC-′3 CBX8 on target sequence with 5′ A:(SEQ ID NO: 37) 5′-ATCAGGAGGGCTTCGGC-′3CBX8 on target sequence with 5′ C: (SEQ ID NO: 38)5′-CTCAGGAGGGCTTCGGC-′3 CBX8 on target sequence with 5′ G:(SEQ ID NO: 39) 5′-GTCAGGAGGGCTTCGGC-′3CBX8 off-target sequence with 5′ T: (SEQ ID NO: 40)5′-TTCATAAGGGATTAGGC-′3 CBX8 off-target sequence with 5′ A:(SEQ ID NO: 41) 5′-ATCATAAGGGATTAGGC-′3CBX8 off-target sequence with 5′ C: (SEQ ID NO: 42)5′-CTCATAAGGGATTAGGC-′3 CBX8 off-target sequence with 5′ G:(SEQ ID NO: 43) 5′-GTCATAAGGGATTAGGC-′3Modified TALE Domains and Proteins that Specifically Target ATM

Some aspects of this disclosure are based on the recognition thatcertain modifications (e.g., mutations or amino acid substitutions)within ATM-targeting TALE proteins or ATM-targeting TALE domainsincrease the specificity of the ATM-targeting TALE protein to anATM-target sequence relative to one or more off-target sequences.Accordingly, some aspects of this disclosure provide proteins withmodified TALE N-terminal domains that target the ATM gene. The ATM geneencodes the ATM serine/threonine kinase and is also referred to as AT1,ATA, ATC, ATD, ATE, ATDC, TEL1, and TELO1. The protein encoded by theATM gene belongs to the PI3/PI4-kinase family. Without wishing to bebound by any particular theory, this protein is a cell cycle checkpointkinase that phosphorylates, and thus, regulates a wide variety ofdownstream proteins, including tumor suppressor proteins p53 and BRCA1,checkpoint kinase CHK2, checkpoint proteins RAD17 and RAD9, and DNArepair protein NBS1. This protein and the closely related kinase ATR arethought to be master controllers of cell cycle checkpoint signalingpathways that are required for cell response to DNA damage and forgenome stability. Mutations in this gene are associated with ataxiatelangiectasia, an autosomal recessive disorder. Accordingly, in someembodiments, the disclosure provides proteins comprising an amino acidsequence that is at least 80% identical to the amino acid sequence ofSEQ ID NO: 1 comprising one or more of amino acid substitutions Q13R,A25E, W126C, and G132R as compared to SEQ ID NO: 1, or a homologousresidue in a canonical N-terminal TALE domain. In some embodiments, theprotein comprises one or more of amino acid substitutions: Q13R, A25E,W126C, and G132R as compared to SEQ ID NO: 1, or a homologous residue ina canonical N-terminal TALE domain.

Some aspects of this disclosure are based on the recognition thatcertain modifications (e.g., mutations or amino acid substitutions)within ATM-targeting TALE proteins or ATM-targeting TALE domainsincrease the specificity of the ATM-targeting TALE protein to an ATMtarget sequence relative to one or more off-target sequences.Accordingly, some aspects of this disclosure provide proteins that bindto an ATM target sequence with at least 5%, at least 10%, at least 15%,at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, atleast 45%, at least 50%, at least 55%, at least 60%, at least 65%, atleast 70%, at least 75%, at least 80%, at least 85%, at least 90%, atleast 95%, at least 10%, at least 150%, at least 200%, at least 250%, atleast 300%, at least 350%, at least 400%, at least 450%, or at least500% greater affinity as compared to an off-target sequence. Theaffinity of the ATM-targeting TALE protein to a target sequence may bedetermined by any suitable method known in the art. In some embodimentsthe affinity of the ATM-targeting TALE protein to the target sequence isdetermined by measuring the binding affinity of the ATM-targeting TALEprotein to the target sequence. In some embodiments the affinity of theATM-targeting TALE protein to the target sequence is determined byindirectly measuring the binding affinity. For example, the bindingaffinity is measured using an indirect readout such as expression of anucleotide sequence (e.g., a gene), cleavage of a nucleotide sequence,or modification of a nucleotide sequence that is responsive to bindingof the ATM-targeting TALE protein to a target sequence.

In some embodiments, the ATM-targeting TALE protein comprises a TALEN.In some embodiments, the ATM-targeting TALEN provided is a monomer. Insome embodiments, the ATM-targeting TALEN monomer can dimerize withanother ATM-targeting TALEN monomer to form an ATM-targeting TALENdimer. In some embodiments the formed dimer is a homodimer. In someembodiments, the dimer is a heterodimer.

In some embodiments, the proteins of the present disclosure comprise anamino acid sequence that is at least 82% identical, at least 84%identical, at least 86% identical, at least 88% identical, at least 90%identical, at least 92% identical, at least 94% identical, at least 95%identical, at least 96% identical, at least 97% identical, at least 98%identical, or at least 99% identical to SEQ ID NO: 1. In someembodiments, the proteins of the present disclosure comprise one or moreof amino acid substitutions Q13R, A25E, W126C, and G132R as compared toSEQ ID NO: 1 or a homologous residue in a canonical N-terminal TALEdomain. It should be appreciated that the proteins of the presentdisclosure may comprise one, or any combination of amino acidsubstitutions including: Q13R, A25E, W126C, and G132R as compared to SEQID NO: 1, or a homologous residue in a canonical N-terminal TALE domain.

In some embodiments, the ATM target sequence comprises the nucleic acidsequence TGAATTGGGATGCTGTTT (SEQ ID NO: 15) and/or the nucleic acidsequence TTTATTTTACTGTCTTTA (SEQ ID NO: 16). In some embodiments, theATM target sequence comprises a left half-site and/or a right half-site.In some embodiments, the left half-site comprises the nucleic acidsequence of (SEQ ID NO: 15). In some embodiments, the right half sitecomprises the nucleic acid sequence of (SEQ ID NO: 16). The ATM targetsequence, in some embodiments, comprises an LSR structure. An LSRstructure has a left half-site (which may bind one monomer of a TALEprotein), a right half-site (which may bind a second monomer of a TALEprotein), and a spacer sequence between the half sites. In the contextof TALE nucleases (TALENs), the spacer sequence may be cut by thenuclease. In some embodiments, the ATM target sequence comprises thestructure ([left half-site]-[spacer sequence]-[right half-site]). Thespacer sequence may be any suitable length for use in accordance withany of the methods provided herein. In some embodiments, the spacersequence is from 2 nucleotides to 100 nucleotides in length. In someembodiments, the spacer sequence is form 5 to 30 nucleotides in length.In some embodiments, the spacer sequence is 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or30 nucleotides in length. In some embodiments the spacer sequencecomprises the nucleic acid sequence TTAGGTATTCTATTCAAA (SEQ ID NO: 25).In some embodiments, the ATM target site comprises the nucleic acidsequence of SEQ ID NO: 35(TGAATTGGGATGCTGTTTTTAGGTATTCTATTCAAATTTATTTTACTGTCTTTA.

In some embodiments, the ATM target site comprises a left half-site. Insome embodiments, the ATM left half-site comprises the nucleic acidsequence of any one of SEQ ID NOs: 17, 19, 21, or 23. In someembodiments, the ATM target site comprises a right half-site. In someembodiments, the ATM right half-site comprises the nucleic acid sequenceof any one of SEQ ID NOs: 18, 20, 22, or 24.

In some embodiments, the protein comprises an amino acid sequence thatis at least 80% identical to the amino acid sequence provided in SEQ IDNO: 13, wherein the amino acid sequence comprises one of the amino acidsubstitutions or combination of amino acid substitutions selected fromQ53R and A252T; W166C, K260R, A398S, A514T, A592V, and Q745P; A252T,Q505K, and Q745P; and A252T, L338S, Q505K, and Q745P; as compared to SEQID NO: 13.

In some embodiments, the protein comprises an amino acid sequence thatis at least 80% identical to the amino acid sequence provided in SEQ IDNO: 13, wherein the amino acid sequence comprises one of the amino acidsubstitutions or combination of amino acid substitutions selected fromA65E and E815G; G172R and A252T; W166C, A398S, A514T, A592V, and P611Q;W166C, A398S, A514T, A592V, and K688R; A252T, K464R, and A568V; andD310E, V640I, and L644F; as compared to SEQ ID NO: 13.

In some embodiments, the protein comprises an amino acid sequence thatis at least 80% identical to the amino acid sequence provided in SEQ IDNO: 13, wherein the amino acid sequence comprises one of the amino acidsubstitutions or combination of amino acid substitutions selected fromA252T, Q505K, R506K, Q745P, and A789V; A252T, Q505K, Q745P, and A789V;and A252T, L338S, Q505K, Q745P, and A789V; as compared to SEQ ID NO: 13.

In some embodiments, the protein comprises an amino acid sequence thatis at least 80% identical to the amino acid sequence provided in SEQ IDNO: 13, wherein the amino acid sequence comprises one of the amino acidsubstitutions or combination of amino acid substitutions selected fromQ53R and A252T; or A252T, L338S, Q505K, and Q745P as compared to SEQ IDNO: 13.

In some embodiments, the protein comprises an amino acid sequence thatis at least 82% identical, at least 84% identical, at least 86%identical, at least 88% identical, at least 90% identical, at least 92%identical, at least 94% identical, at least 95% identical, at least 96%identical, at least 97% identical, at least 98% identical, or at least99% identical to the amino acid sequence provided in SEQ ID NO: 13comprising any of the amino acid substitutions provided herein.

Some aspects of this disclosure are based on the recognition thatcertain modifications (e.g., mutations or amino acid substitutions)within ATM targeting TALE proteins or ATM targeting TALE arrays increasethe specificity of the ATM targeting TALE protein to an ATM targetsequence relative to one or more off-target sequences. Accordingly, someaspects of this disclosure provide proteins with modified TALE repeatarrays. In some embodiments, the disclosure provides proteins comprisingan amino acid sequence that is at least 80% identical to the amino acidsequence of SEQ ID NO: 12 comprising one or more of amino acidsubstitutions A76T, K84R, D134E, L162S, A222S, K288R, Q329K, R330K,A338T, A392V, A416V, P435Q, V464I, L468F, and K512R as compared to SEQID NO: 12.

In some embodiments, the proteins of the present disclosure comprise anamino acid sequence is at least 82% identical, at least 84% identical,at least 86% identical, at least 88% identical, at least 90% identical,at least 92% identical, at least 94% identical, at least 95% identical,at least 96% identical, at least 97% identical, at least 98% identical,or at least 99% identical to SEQ ID NO: 12. In some embodiments, theproteins of the present disclosure comprise a TALE repeat arraycomprising one or more of the amino acid substitutions or combination ofamino acid substitutions selected from A76T; A76T and Q329K; A76T,L162S, and Q329K; and K84R, A222S, A338T, and A416V; as compared to SEQID NO: 12. In some embodiments, the proteins of the present disclosurecomprise a TALE repeat array comprising one or more of the amino acidsubstitutions or combination of amino acid substitutions selected fromA76T; A76T, K288R, and A392V; D134E, V464I, and L468F; A222S, A338T,A416V, and P435Q; and A222S, A338T, A416V, and K512R; as compared to SEQID NO: 12. In some embodiments, the proteins of the present disclosurecomprise a TALE repeat array comprising one or more of the amino acidsubstitutions or combination of amino acid substitutions selected from:A76T, Q329K and R330K; A76T and Q329K; A76T, L162S, and Q329K; and A76Tand Q329K; as compared to SEQ ID NO: 12. In some embodiments, theproteins of the present disclosure comprise a TALE repeat arraycomprising one or more of the amino acid substitutions or combination ofamino acid substitutions selected from A76T; and A76T, L162S, and Q329K;as compared to SEQ ID NO: 12.

Expression Constructs

Some aspects of this disclosure provide nucleic acids encoding any ofthe TALEs provided herein. In some embodiments, the nucleic acidsencoding the TALEs are under the control of a heterologous promoter. Insome embodiments, the encoding nucleic acids are included in anexpression construct, e.g., a plasmid, a viral vector, or a linearexpression construct. In some embodiments, the nucleic acid orexpression construct is in a cell, tissue, or organism.

Nucleic acids encoding any of the proteins, described herein, may be inany number of nucleic acid “vectors” known in the art. As used herein, a“vector” means any nucleic acid or nucleic acid-bearing particle, cell,or organism capable of being used to transfer a nucleic acid into a hostcell. The term “vector” includes both viral and nonviral products andmeans for introducing the nucleic acid into a cell. A “vector” can beused in vitro, ex vivo, or in vivo. Non-viral vectors include plasmids,cosmids, artificial chromosomes (e.g., bacterial artificial chromosomesor yeast artificial chromosomes) and can comprise liposomes,electrically charged lipids (cytofectins), DNA-protein complexes, andbiopolymers, for example. Viral vectors include retroviruses,lentiviruses, adeno-associated virus, pox viruses, baculovirus,reoviruses, vaccinia viruses, herpes simplex viruses, Epstein-Barrviruses, and adenovirus vectors, for example. Vectors can also comprisethe entire genome sequence or recombinant genome sequence of a virus. Avector can also comprise a portion of the genome that comprises thefunctional sequences for production of a virus capable of infecting,entering, or being introduced to a cell to deliver nucleic acid therein.

Expression of any of the proteins, described herein, may be controlledby any regulatory sequence (e.g. a promoter sequence) known in the art.Regulatory sequences, as described herein, are nucleic acid sequencesthat regulate the expression of a nucleic acid sequence. A regulatory orcontrol sequence may include sequences that are responsible forexpressing a particular nucleic acid (e.g., a nucleic acid encoding aTALE) or may include other sequences, such as heterologous, synthetic,or partially synthetic sequences. The sequences can be of eukaryotic,prokaryotic or viral origin that stimulate or repress transcription of agene in a specific or non-specific manner and in an inducible ornon-inducible manner. Regulatory or control regions may include originsof replication, RNA splice sites, introns, chimeric or hybrid introns,promoters, enhancers, transcriptional termination sequences, poly Asites, locus control regions, signal sequences that direct thepolypeptide into the secretory pathways of the target cell, and introns.A heterologous regulatory region is not naturally associated with theexpressed nucleic acid it is linked to. Included among the heterologousregulatory regions are regulatory regions from a different species,regulatory regions from a different gene, hybrid regulatory sequences,and regulatory sequences that do not occur in nature, but which aredesigned by one of ordinary skill in the art.

The term operably linked refers to an arrangement of sequences orregions wherein the components are configured so as to perform theirusual or intended function. Thus, a regulatory or control sequenceoperably linked to a coding sequence is capable of affecting theexpression of the coding sequence. The regulatory or control sequencesneed not be contiguous with the coding sequence, so long as theyfunction to direct the proper expression or polypeptide production.Thus, for example, intervening untranslated but transcribed sequencescan be present between a promoter sequence and the coding sequence andthe promoter sequence can still be considered operably linked to thecoding sequence. A promoter sequence, as described herein, is a DNAregulatory region a short distance from the 5′ end of a gene that actsas the binding site for RNA polymerase. The promoter sequence may bindRNA polymerase in a cell and/or initiate transcription of a downstream(3′ direction) coding sequence. The promoter sequence may be a promotercapable of initiating transcription in prokaryotes or eukaryotes. Somenon-limiting examples of eukaryotic promoters include thecytomegalovirus (CMV) promoter, the chicken (3-actin (CBA) promoter, anda hybrid form of the CBA promoter (CBh).

Kits

Some aspects of this disclosure provide kits comprising an engineeredTALE or TALE domain as provided herein, a cloning vector that encodes anengineered TALE or TALE domain as provided herein, or a composition(e.g., a pharmaceutical composition) comprising such a TALE. In someembodiments, the kit comprises a cloning vector comprising a nucleicacid sequence that encodes any of the engineered N-terminal TALEdomains, any of the engineered C-terminal TALE domains, and/or any ofthe TALE repeat arrays provided herein. In some embodiments, the kitcomprises a cloning vector comprising a nucleic acid sequence thatencodes an engineered N-terminal TALE domain, and/or an engineeredC-terminal TALE domain, provided herein. Such cloning vectors may beused to clone (e.g., using standard molecular biology techniques) in anyTALE repeat array to specifically target any sequence of interest. Insome embodiments, the kit comprises an excipient and instructions forcontacting the TALE with the excipient to generate a compositionsuitable for contacting a nucleic acid with the TALE. In someembodiments, the excipient is a pharmaceutically acceptable excipient.

Typically, the kit will comprise a container housing the components ofthe kit, as well as written instructions stating how the components ofthe kit should be stored and used.

Methods

Some aspects of this disclosure provide methods for phage-assisted,continuous evolution of a DNA binding domains. In some embodiments, themethods comprise a negative selection against an undesired activity ofthe DNA-binding domain, e.g., a binding activity towards an off-targetsite. Such negative selection strategies can be used to improve thespecificity of a DNA binding domain being evolved, e.g., in that bindingto off-target sites is minimized or abolished. In some embodiments, themethods comprise a negative selection against a plurality of undesiredactivities, e.g., against binding activity towards a plurality ofoff-target sites. In some embodiments, the methods comprise a negativeselection that is performed simultaneous to a positive selection, e.g.,in a lagoon comprising host cells harboring both a positive and anegative selection construct, or in a lagoon harboring different hostcells, e.g., host cells comprising a positive selection construct andhost cells harboring a negative selection construct. In someembodiments, a plurality of negative selections is carried outsimultaneously, e.g., in a lagoon comprising host cells harboring aplurality of different negative selection constructs, or in a lagoonharboring different host cells comprising different negative selectionconstructs. In some embodiments, the negative selection comprises aselection, either sequentially or simultaneously, against at least 1, atleast 2, at least 3, at least 4, at least 5, at least 6, at least 7, atleast 8, at least 9, at least 10, at least 20, at least 30, at least 40,at least 50, at least 60, at least 70, at least 80, at least 90, or atleast 100 different off-target sites.

In some embodiments, the methods for phage-assisted, continuousevolution of a DNA binding domain comprise identifying of-target sitesthat the DNA binding domain binds to. In some embodiments, suchoff-target sites are identified using high-throughput methods, e.g.,library screening methods that identify off-target sites bound by theDNA binding domain from a library of candidate binding sites. Suitablelibrary screening methods are disclosed herein, and additional suitablemethods will be apparent to those of skill in the art based on thepresent disclosure. Exemplary suitable high-throughput methods foridentifying off-target binding sites include, without limitation, thosedisclosed in International Patent Application WO2013/066438, the entirecontents of which are incorporated herein by reference.

In some embodiments, the methods for phage-assisted, continuousevolution of a DNA binding domain provided herein comprise (a)contacting a flow of host cells through a lagoon with a selection phagecomprising a nucleic acid sequence encoding a DNA-binding domain to beevolved, and (b) incubating the selection phage or phagemid in the flowof host cells under conditions suitable for the selection phage toreplicate and propagate within the flow of host cells, and for thenucleic acid sequence encoding the DNA-binding domain to be evolved tomutate. In some embodiments, the host cells are introduced through thelagoon at a flow rate that is faster than the replication rate of thehost cells and slower than the replication rate of the phage, therebypermitting replication and propagation of the selection phage in thelagoon. In some embodiments, the flow of host cells comprises aplurality of host cells harboring a positive selection constructcomprising a nucleic acid sequence encoding a gene product essential forthe generation of infectious phage particles, wherein the gene productessential for the generation of infectious phage particles is expressedin response to a desired DNA-binding activity of the DNA-binding domainto be evolved or an evolution product thereof. In some embodiments, theselection phage does not comprise a nucleic acid sequence encoding thegene product essential for the generation of infectious phage particles.In some embodiments, the flow of host cells comprises a plurality ofhost cells harboring a negative selection construct comprising a nucleicacid sequence encoding a dominant negative gene product that decreasesor abolishes the production of infectious phage particles, wherein thedominant negative gene product is expressed in response to an undesiredactivity of the DNA-binding domain to be evolved or an evolution productthereof.

Some aspects of this disclosure provide methods for improving thespecificity of a DNA-binding domain by phage-assisted, continuousevolution. The method comprises, in some embodiments, (a) contacting aflow of host cells through a lagoon with a selection phage comprising anucleic acid sequence encoding a DNA-binding domain to be evolved, and(b) incubating the selection phage or phagemid in the flow of host cellsunder conditions suitable for the selection phage to replicate andpropagate within the flow of host cells, and for the nucleic acidsequence encoding the DNA-binding domain to be evolved to mutate. Insome embodiments, the host cells are introduced through the lagoon at aflow rate that is faster than the replication rate of the host cells andslower than the replication rate of the phage, thereby permittingreplication and propagation of the selection phage in the lagoon. Insome embodiments, the flow of host cells comprises a plurality of hostcells harboring a negative selection construct comprising a nucleic acidsequence encoding a dominant negative gene product that decreases orabolishes the production of infectious phage particles, wherein thedominant negative gene product is expressed in response to an undesiredactivity of the DNA-binding domain to be evolved or an evolution productthereof.

In some embodiments of the PACE methods disclosed herein, the positiveselection construct and/or the negative selection construct is comprisedon an accessory plasmid. In some embodiments, the flow of host cellscomprises a plurality of different negative selection constructs,wherein in each different negative selection construct, the dominantnegative gene product is expressed in response to a different undesiredactivity of the DNA-binding domain to be evolved or an evolution productthereof. In some embodiments, the different negative selectionconstructs are comprised in different host cells within the flow of hostcells.

In some embodiments, the method further comprises (i) identifying aplurality of undesired activities of the DNA-binding domain to beevolved or an evolution product thereof, and (ii) providing a pluralityof different negative selection construct selecting against differentundesired activities identified in (i), wherein each different negativeselection construct selects against a different undesired activity. Insome embodiments, the undesired activity is DNA-binding of an off-targetsequence. In some embodiments, the identifying of (i) comprisesperforming a high-throughput screen of candidate off-target sequences.

In some embodiments, the dominant negative gene product is expressed inresponse to DNA-binding of an off-target sequence by the DNA-bindingdomain to be evolved or an evolution product thereof. In someembodiments, the different negative selection constructs comprisedifferent off-target sequences. In some embodiments, the DNA-bindingdomain is a TALE domain.

The scope of this disclosure also embraces methods of using the TALEsprovided herein. It will be apparent to those of skill in the art thatthe TALEs provided herein can be used in any method suitable for theapplication of TALEs, including, but not limited to, those methods andapplications known in the art. Such methods may include TALE-mediatedmodulation of gene expression or TALE-mediated cleavage of DNA, e.g., inthe context of genome manipulations such as, for example, targeted geneknockout through non-homologous end joining (NHEJ) or targeted genomicsequence replacement through homology-directed repair (HDR) using anexogenous DNA template, respectively. The improved features of the TALEsprovided herein, e.g., the improved specificity of some of the TALEsprovided herein, will typically allow for such methods and applicationsto be carried out with greater efficiency. For example, and withoutlimitation, the instant disclosure provides the use of the TALENsprovided herein in any method suitable for the use of TALEs (e.g.,TALENs) as described in Boch, Jens (February 2011). “TALEs of genometargeting”. Nature Biotechnology 29 (2): 135-6. doi: 10.1038/nbt.1767.PMID 21301438; Boch, Jens; et. al. (December 2009). “Breaking the Codeof DNA Binding Specificity of TAL-Type III Effectors”. Science 326(5959): 1509-12. Bibcode:2009Sci . . . 326.1509B.doi:10.1126/science.1178811. PMID 19933107; Moscou, Matthew J.; Adam J.Bogdanove (December 2009). “A Simple Cipher Governs DNA Recognition byTAL Effectors”. Science 326 (5959): 1501. Bibcode:2009Sci . . .326.1501M. doi:10.1126/science.1178817. PMID 19933106; Christian,Michelle; et. al. (October 2010). “Targeting DNA Double-Strand Breakswith TAL Effector Nucleases”. Genetics 186 (2): 757-61.doi:10.1534/genetics.110.120717. PMC 2942870. PMID 20660643; Li, Ting;et. al. 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Aspects of the disclosure embrace methods for using any of the TALEproteins provided herein. In some embodiments, the methods includecontacting a nucleic acid molecule, comprising a target sequence, with aTALE protein provided herein under conditions suitable for the proteinto bind the target sequence. In some embodiments, the method comprisescontacting the nucleic acid molecule in vitro. In some embodiments, themethod comprises contacting the nucleic acid molecule in vivo. In someembodiments, the method comprises contacting the nucleic acid moleculein a cell. In some embodiments, the cell is a cell in vitro. In someembodiments, the cell is a cell in a subject. In some embodiments, themethod comprises contacting the nucleic acid molecule in a subject. Insome embodiments, the nucleic acid molecule is comprised in a genome. Insome embodiments, the target sequence is comprised in or is in proximityto a gene known to be associated with a disease or disorder. In someembodiments, the disease or disorder is a proliferative disease ordisorder. In some embodiments, the proliferative disease or disorder iscancer. In some embodiments, the gene associated with a disease ordisorder is CBX8, ATM or CCR5. In some embodiments, the disease ordisorder is acquired immunodeficiency syndrome (AIDS), or a humanimmunodeficiency virus (HIV) infection. In some embodiments, the targetsequence comprises a left half-site. In some embodiments, the targetsequence comprises a right half-site. In some embodiments, the targetsequence comprises a left half-site and a right half-site. In someembodiments, the left half-site and/or the right half-site comprise anadenine (A), a cytosine (C), or a guanine (G) at the 5′ position. Insome embodiments, the left half-site and/or the right half-site comprisea thymine (T) at the 5′ position. In some embodiments, the proteincomprises an effector domain. In some embodiments, the effector domaincomprises a nuclease domain (e.g., a Fok1 domain). In some embodiments,the nuclease domain is a FokI nuclease domain and/or wherein the proteinis a TALEN. In some embodiments, the protein cleaves the target sequencewhen the protein is bound to the target sequence. In some embodiments,the protein dimerizes to cleave the target sequence. In someembodiments, the effector domain comprises a transcriptional activatoror repressor domain, a recombinase domain, or an epigenetic modificationenzyme domain. In some embodiments, the protein modulates transcriptionof the gene known to be associated with a disease or disorder. In someembodiments, the protein increases transcription of the gene known to beassociated with a disease or disorder. In some embodiments, the proteindecreases transcription of the gene known to be associated with adisease or disorder. In some embodiments, the protein prohibitstranscription of the gene known to be associated with a disease ordisorder.

In some embodiments, the methods of the present disclosure includeadministering any of the proteins, provided herein, to a subject havingor diagnosed with a disease or disorder in an amount effective toameliorate at least one symptom of the disease or disorder. In someembodiments, the disease or disorder is a proliferative disease. In someembodiments, the disease or disorder is cancer. In some embodiments, thedisease or disorder is acquired immunodeficiency syndrome (AIDS), or ahuman immunodeficiency virus (HIV) infection. In some embodiments, thedisease or disorder is a monogenic disease that is associated with agenetic defect in a single gene that can be addressed with a nuclease,e.g., a TALEN, or a ZFN.

EXAMPLES

Introduction

A system was developed that enables proteins to evolve continuously inthe laboratory with virtually no researcher intervention³¹. Theresulting system, phage-assisted continuous evolution (PACE), allowsproteins to undergo directed evolution at a rate ˜100-fold faster thanconventional methods (FIG. 1A). During PACE, host E. coli cellscontinuously dilute an evolving population of filamentous bacteriophages(“selection phage”, SP) in a fixed-volume vessel (a “lagoon”). Dilutionoccurs faster than cell division but slower than phage replication,ensuring that only the phage can accumulate mutations. Each SP carriesan evolving gene instead of gene III, an essential phage gene that isrequired for infection. Phage encoding active variants trigger host-cellexpression of gene III from the “accessory plasmid” (AP) and produceinfectious progeny, while phage encoding less active variants producenon-infectious progeny that are diluted out of the lagoon. PACE has beenused to rapidly evolve RNA polymerases and proteases with tailor-madeproperties³¹³⁵. It was tested whether the PACE system could be adaptedto evolve DNA-binding domains with altered or improved DNA-bindingspecificity.

Presented herein is a general system for the continuous evolution ofDNA-binding domains, DNA-binding PACE (DB-PACE). Using the previouslydescribed PACE platform as a starting point, described herein, is thedevelopment of positive and negative PACE selections for DNA binding,optimization of host cell flow rates and background activity levels, andintegration of these advances to enable for the first time thecontinuous evolution of DNA-binding activity. The system was validatedby evolving restored DNA-binding activity in mutated zinc fingers. Thesystem was then applied to evolve TALEs that prefer a non-canonical 5′nucleotide (A, C, or G) over the native 5′ T. Finally, this system wasused to evolve TALE proteins with enhanced DNA specificity by selectingvariants that maintain on-target DNA binding but lose affinity for theirmost highly cleaved off-target site in human cells. The improved DNAcleavage specificity of the corresponding TALENs was verified both invitro using high-throughput specificity profiling, and in human cells.The results establish DB-PACE as a new strategy for tuning the affinityand specificity of DBDs including genome-editing proteins, identifysubstitutions in TALE proteins that determine DNA-binding preferences,and expand the scope of continuous protein evolution.

Example 1 Development of a PACE System for DNA-Binding Activity

To develop a PACE-compatible DNA-binding selection, a DNA-binding domainof interest was linked to a subunit of bacterial RNA polymerase III(RNAP). It was intended that binding of this fusion protein to operatorsequences upstream of a minimal lac promoter would induce transcriptionof a downstream gene III-luciferase reporter through recruitment orstabilization of the RNAP holoenzyme (FIG. 1B). To validate thisstrategy, an assay was developed that transduces cognate DNA-binding ofthe DBD from Zif268 (residues 333-420)³⁷, expressed from atetracycline-inducible promoter, into activation of pIII-luciferaseexpression. This assay was used to evaluate a variety of DNA operatorlocations (at −55 and −62 bp with respect to the transcriptioninitiation site)^(36,38) and RNA polymerase fusion architectures. Fusingthe RNAP ω subunit to the N-terminus of Zif268 with an 11-residue linkerresulted in ≥10-fold increase in pIII-luciferase production when theconsensus Zif268 binding site (5′-GCGTGGGCG-3′; SEQ ID NO: 48) waspositioned at −62 (FIG. 5). To test the DNA specificity of this system,a control construct with an off-target Zif268 binding site was createdin which the middle triplet of the target DNA site was changed to5′-TTA-3′¹⁰. Only E. coli containing the reporter downstream of theon-target sequence, but not those containing the off-target sequence,produced pIII-luciferase (FIG. 1C), establishing sequence-specific andDNA binding-dependent gene expression. the consensus Zif268 binding site(5′-GCGTGGGCG-3′; SEQ ID NO: 48) was positioned at −62 (FIG. 5A). Totest the DNA specificity of this system, a control construct with anoff-target Zif268 binding site was created in which the middle tripletof the target DNA site was changed to 5′-TTA-3′¹⁰. Only E. colicontaining the reporter downstream of the on-target sequence, but notthose containing the off-target sequence, produced pIII-luciferase (FIG.1C), establishing sequence-specific and DNA binding-dependent geneexpression.

To integrate this system into PACE, the DNA operator-gene III-luciferasecassette was moved to an AP, and moved the RNAP w-Zif268 protein to anSP. Next, an E. coli strain designated S2060 was developed capable ofinducing LacZ in response to activation of the phage shock promoter, atranscriptional regulatory element that responds to a number ofenvironmental signals including filamentous phage infection (FIGS.6A-8C). This strain can be used in combination with colorimetric LacZsubstrates such as X-gal to stain bacteria that have been infected withphage. It was tested whether w-Zif268-SP could propagate in aDNA-binding activity-dependent manner on S2060 cells containing an APwith the cognate Zif268 binding sequence, or a mutated binding sequence.A robust formation of colored plaques was observed, indicative of phagepropagation, on cells harboring the on-target AP, but not on cellsharboring an AP containing the off-target sequence (FIG. 9A). Theseobservations demonstrate DNA binding activity-dependent phagepropagation. Next, an initial PACE experiment was performed to optimizethe SP backbone. SPs encoding Zif268 in PACE over 24 h were continuouslypropagated on host cells carrying the cognate AP plasmid and amutagenesis plasmid (MP)³¹. After 24 h of PACE, the surviving SPscontained mutations in the phage genes encoding pII/X and pIV, and thefusion protein linker (FIG. 9B). These results collectively establish abasis for the continuous evolution of DBDs using PACE.

To validate the ability of this positive selection PACE system toimprove DNA-binding activity, the system was used to evolve DNA bindingin an inactive Zif268 mutant protein. Mutation of Arg24 in Zif268 to asmall hydrophobic residue is known to abrogate DNA binding⁴⁰. A lagoonwas seeded with inactive w-Zif268 SP containing an R24V mutation. After24 h of neutral drift (mutation in the absence of any selectionpressure) followed by 24 h of PACE on host cells containing the cognateAP, the evolved SPs were capable of propagating on the target AP (FIG.9C). All of the sequenced phage clones at the end of the 24-h PACEexperiment contained the V24R reversion mutation using an Arg codon notpresent in the wild-type gene (AGA vs. CGC) (FIG. 9D). Collectively,these results validate that this system can rapidly evolve proteins withDNA-binding activity.

Example 2: Continuous Evolution of TALE 5′ Specificity

This system was used to continuously evolve TALE proteins with novelproperties. A series of C-terminal fusions between a previously reportedTALE array targeting CBX8 (right half-site TALE)¹⁸, and the RNAP cosubunit were tested. Fusions using a linker of 18 or 28 amino acids ofthe natural TALE C-terminus followed by a GGGGS sequence resultedin >10-fold gene activation in a luciferase assay (FIG. 10A). Thesequence specificity of the system was verified using an off-targetsequence in the luciferase assay, and performed on- and off-targetcolorimetric plaque assays using TALE-ω SP and host cells harboring theAP containing the target CBX8 sequence. Similar to the findings withzinc fingers, both luciferase expression and phage propagation weredependent on the presence of the cognate TALE binding site (FIG. 10B).Finally, PACE was performed for 24 h on the cognate AP to optimize theSP backbone. This experiment resulted in several mutations in the phagegenome, as well as an A8V substitution in the ωRNAP subunit (FIG. 10C).These observations collectively suggest the applicability of DB-PACE toTALE proteins.

One of the limitations of canonical TALE arrays is that target sequencesmust begin with a 5′ T for optimal binding^(13,14). PACE was used toevolve TALE proteins with altered 5′ nucleotide preferences, both toexpand the DNA sequences that can be targeted with TALEs withoutcompromising DNA-binding activity, and to illuminate TALE domainstructure-function relationships that contribute to 5′ specificity. The5′ DNA specificity of the CBX8-targeting TALE was examined using thegene III-luciferase reporter assay. We observed 2- to 3-fold higherluciferase induction for 5′ T over the other bases (FIG. 10D). Next, APswere created in which the 5′ base of the cognate sequence was changed to5′ A, 5′ C, or 5′ G, and initiated three parallel PACE experiments toevolve TALEs with increased DNA-binding activity for each of thesesequences (FIG. 2A). For each experiment, we performed selections induplicate lagoons (L1 and L2). Following 48 h of PACE, we isolated phagewith up to 6-fold increased activity on 5′ A relative to the canonicalTALE protein (FIG. 2B), 5-fold increased activity on 5′ C (FIG. 11A),and 5-fold higher activity on 5′ G target sequences (FIG. 11B).

Analysis of individual clones from these three evolutions experimentsrevealed a variety of mutations occurring throughout the entire TALEprotein sequence (FIG. 2B and FIG. 11A, 11B). High-throughput sequencingof ˜10⁵ phage revealed that TALE mutations A79E (62% L2), A133E (33%L2), E622K (60% L1, 37% L2), and Q711P (28% L2), were prevalent in 5′ Alagoons (FIG. 12A), while A79E (78% L2), L508F (77% L2), and K634R (74%L) were dominant in 5′ C lagoons (FIG. 12B), and D7Y (97% L), G565S (97%L), and E622K (97% L) were predominant in the 5′ G lagoon (FIG. 12C). Inaddition, V767G, corresponding to V38G in the RNAP co subunit, wascommon among phage evolved in the 5′ A and 5′ G lagoons (FIG. 12A, 12C).Combined with structure-activity analyses (FIG. 13), these data revealsubstitutions that alter TALE 5′ nucleotide specificity and bindingactivity, and highlight the value of unbiased mutagenesis in DB-PACEthat allows the discovery of neutral and beneficial amino acidsubstitutions that cannot be easily predicted a priori.

Previous attempts to evolve 5′ TALE specificity using traditionaldirected evolution methods did not achieve specific recognition of 5′ Aor 5′ C^(28, 29). To assay the specificity of the evolved phage pools, aseries of plaque assays were performed using cells carrying APs withbinding sequences beginning with a 5′ A, C, G, or T. This assay revealedthat the activity of evolved CBX8-targeting TALEs was increased in apromiscuous manner, as expected given the absence of acounter-selection, and was not specific to any 5′ nucleotide (FIG. 14A).To evolve selective recognition of non-T 5′ nucleotides, a negativeselection strategy was adapted that links undesired activities to theproduction of pIII-neg, a dominant negative pIII variant that poisons,rather than enables, phage propagation³³.

A series of negative selection APs (APNegs) were designed in whichbinding of a TALE-ω fusion protein to an off-target DNA sequence inducesexpression of gene III-neg (encoding pIII-neg) fused to yellowfluorescent protein (YFP) from a minimal lac promoter (FIG. 2C). Toenable tuning of negative selection stringency, a theophylline-inducibleriboswitch was placed upstream of gene III-neg-YFP. Next, cells carryingan AP requiring recognition of a 5′A-CBX8 sequence were generated, incombination with one of three APNegs bearing 5′ C-, G-, or T-CBX8sequences. Using the TALE-ω SP evolved to bind to the 5′ A sequence,plaque assays were performed on each of these strains in the presence ofincreasing doses of theophylline to modulate pIII-neg productionresulting from binding to 5′ C, G, or T sequences in the correspondingAPNeg. It was confirmed that phage propagation could be suppressed in anactivity- and theophylline-dependent manner (FIG. 14B, 14C). Together,these results establish a negative selection system for DB-PACE.

This negative selection system was applied to evolve TALE domains thatpreferentially bind a 5′ A target site over a 5′ T using simultaneouspositive and negative selection in PACE. To perform simultaneousmultiplexed negative selection against binding of target DNA sequencesbeginning with 5′ C, G, or T, three E. coli strains were mixed in equalproportion, each carrying an APNeg plasmid containing a 5′ C, G, or Toff-target sequence, together with a positive selection AP harboring the5′ A target site and an MP. The resulting mixed host cell population wasused in a 144-h PACE experiment in which phage surviving the previous 5′A PACE experiment were subjected to increasing levels of negativeselection stringency (+0.1 mM theophylline every 48 h).

Several TALE-encoding genes surviving 144 h of dual positive andnegative PACE were cloned into tetracycline-inducible expressionplasmids and transformed each of them into four distinct cell strainscontaining APNeg plasmids with a CBX8 binding site starting with 5′ A,C, G, or T, to assay their 5′ specificity. Measurement ofanhydrotetracycline (ATc)-induced YFP fluorescence revealed that allclones displayed substantial (>2-fold) increase in DNA-binding activityon sequences beginning with 5′ A, 5′ C, and 5′ G, and that clones fromlagoon 2 (L2) displayed a two-fold reduction in binding affinity for thecanonical 5′ T site, resulting in a ˜4-fold 5′ A vs. T specificitychange relative to the canonical TALE protein (FIG. 2D). These resultssuggest stronger selection against binding 5′ T sequences and weakerselection pressure against binding sequences starting with 5′ C or 5′ G.This outcome likely resulted from negative selection against the 5′Tsequence engaging earlier in the 144 h experiment than negativeselection on the 5′ C and 5′ G sequences. Consistent with thishypothesis, in vitro plaque assays showed that a low dose oftheophylline (0.2 mM) is sufficient to suppress evolved 5′-A phagepropagation on cells carrying a 5′ T-CBX8 sequence, while a higher dose(0.4 mM) is required to block propagation on 5′ C or 5′ G sequences(FIG. 14C). Based on the theophylline titration schedule, phageexperienced ˜48 h of negative selection against the 5′ T sequence, butonly 24 h against the 5′ C and 5′ G sequences. While differences in thegenotypes and phenotypes observed in L1 and L2 reflects the stochasticnature of protein evolution, 100% of the evolved TALEs assayed followingnegative selection exhibited preferences for 5′ A over 5′ T (FIG. 2D).

Sequencing ten individual clones from the end of the experiment revealedan average of nine amino acid substitutions distributed throughout eachprotein (FIGS. 2D and 15A), and high-throughput sequence analysis ofphage pool genotypes revealed six predominant amino acid substitutions(K59E, Q513K, N562H, E622K, Q711P, V767G) in the 144 h population (FIG.15B). Of these, only K59E and Q513K (FIG. 16A, 16B) emerged exclusivelyfollowing negative selection, and only the N-terminal substitution K59Ewas amenable to study using site-directed mutagenesis due to the highlyrepetitive nature of TALE repeat arrays. It was found that when presentin isolation on the CBX8 TALE K59E decreases affinity for the 5′ Ttarget sequence by 2-fold, but has little effect on sequences beginningwith 5′ A, C, or G (FIG. 16C). To test if the effect of the K59Emutation is CBX8-TALE context-dependent, or if the mutation alters TALEspecificity in a general manner, this mutation was introduced to adifferent TALE protein targeting the ATM locus (see Table 2 for targetsequences) and assayed the activity of the resulting mutant on thecorresponding 5′ A, C, G, or T target sequences. The K59E substitutionin the ATM TALE increased activity on both 5′ A and 5′ T sequences by afactor of 2 and 1.5-fold, respectively, indicating that while thisposition impacts 5′ specificity in both TALE proteins, the manner inwhich the K59E mutation affects DNA binding is context-dependent (FIG.16D). These results collectively show that coupled positive and negativeselection DB-PACE can rapidly alter TALE 5′ DNA specificity in acontext-dependent manner by maintaining TALE activity on a sitecontaining a target 5′ nucleotide while evolving mutations that decreasebinding to other 5′ off-target sequences.

TABLE 2 Full target sequences used to study ATM TALENs^(a).^(a)For in vitro cleavage assays, left and right half-site recognitionsequences were separated by a constant 18-bp constant spacersequence (5′-TTAGGTATTCTATTCAAA-′3) (SEQ ID NO: 25). For high-throughput specificity profiling, a range of spacer lengths wasused in the library³⁰. ^(b)For the right half-site the sense strandis displayed. SEQ SEQ ID ID Sequence Left-half sequence NO:Right-half sequence^(b) NO: On-target TGAATTGGGATGCTGTTT 15TTTATTTTACTGTCTTTA 16 OffA1 TGAATaGGaAataTaTTT 17 TTTATTTTACTGTtTTTA 18OffA11 TGAATTGaGAgaagcaTT 19 TTTATTTTAtTaTtTTTA 20 OffA17gGAAaTGGGATaCTGagT 21 TTTATgTTACTaTtTcTA 22 OffA23 TagATTGaaATGCTGTTT 23TTTtTaTTAtTaTtTTTA 24

Example 3: Continuous Evolution of Improved TALEN Specificity

TALE arrays are frequently used in the context of TALENs to initiategenome editing⁷. The DNA cleavage specificity of TALENs is imperfect,and off-target DNA sites can undergo TALEN-mediated modification atappreciable levels both in vitro and in human cells^(30,42,43) thatcompromise their usefulness as research tools and potential humantherapeutics. It was determined whether DB-PACE could be used to evolveTALEs with improved specificity for a given target sequence bydecreasing recognition of specific off-target genomic sequences whilemaintaining recognition of the on-target sequence. Off-target genomicsequences can be identified using in vitro high-throughput specificityprofiling^(30,44,45) or other approaches^(20, 42,46,47).

To validate the ability of DB-PACE to improve TALEN specificity, a TALENpair that targets a 36-bp sequence within the human ATM locus was used(see Table 2 for target sequences) for which off-target cleavage sitesin human cells³⁰ were previously identified. An SP encoding the TALEspecifying recognition of the 18-bp left half-site (ATM-L) fused to theco RNAP subunit was generated, and an AP containing the ATM on-targetbinding sequence. Next, an APNeg with an 18-bp operator sequencecorresponding to the left half site of OffA17 was generated, which isthe most frequently cleaved known off-target sequence of this TALEN inthe human genome³⁰. OffA17 differs from the on-target ATM site at fivenucleotide positions (FIG. 3A). Both the positive selection AP and thenegative selection APNeg were co-transformed into host cells to enablesimultaneous positive and negative selection during PACE.

Using these cells, DB-PACE was performed on the ATM-L TALE in duplicatelagoons (L1 and L2) at a flow rate of 1.3 vol/h. Increasing quantitiesof theophylline were added to each lagoon from a starting dose of 0 mMto a final dose of 0.4 mM (+0.1 mM every 24 h) to successively increasenegative selection stringency. At 120 h, the evolved phage populationsfrom L and L2 were pooled, and subjected the mixture to a subsequent 24h PACE experiment in a single lagoon (L3) using a fixed concentration of0.4 mM theophylline and a higher lagoon flow rate of 2.0 vol/h.

Several evolved TALE proteins emerging from L1, L2, and L3 were assayedin the context of the ATM TALEN pair using the in vitro DNA cleavagespecificity profiling assay³⁰. The canonical TALEN pair before evolutionexhibited robust cleavage in vitro of the on-target sequence (31.5%cleavage at a concentration of 12 nM after 90 min) and substantialcleavage of the off-target sequence OffA17 (9.5% cleavage under the sameconditions) (FIG. 3B). In contrast, TALEN pairs containing the evolvedATM-L TALEs from L1 or L3 retained on-target DNA cleavage activitycomparable to that of the canonical TALEN, but exhibited virtually nodetectable cleavage of OffA17 under these conditions (FIG. 3B). The L3evolved clones showed at least 16-fold higher (bounded by the limit ofdetection) on-target:OffA17 off-target cleavage specificity in vitrothan the canonical TALEN (FIG. 3B). Importantly, the on-targetactivities of the canonical and L3-2 TALEN pairs were comparable,indicating that on-target activity was not reduced by DB-PACE (FIG. 17).Indeed, luciferase assay of evolved ATM-L-TALEs in the context of cosubunit fusions revealed that they exhibited 2- to 3-fold higheractivity on the on-target site than the canonical ATM-TALE, but nodetectable activity on the OffA17 site (FIG. 18A). Taken together, thesefindings demonstrate the successful continuous evolution of TALEproteins with greatly improved on-target:off-target DNA specificitiestogether with preserved or enhanced on-target DNA-binding activity.

Sequencing of several evolved ATM-L TALEs revealed a variety ofmutations in L1 and L2 (FIGS. 3B and 18B), but a fairly converged L3population characterized by A252T, L338S, Q505K, and Q745P (FIGS. 3B and18C). Analysis of a series of evolved clones revealed that while Q53R incombination with A252T improved specificity substantially, A252T incombination with Q505K, L338S, and Q745P improved specificity by anadditional >2-fold (FIG. 18D). Although the highly repetitive nature ofTALE array genes precludes site-directed mutagenesis studies on residueswithin repeats, we identified an ATM-L TALE variant containing only asingle A252T mutation. This mutation in isolation exhibited on-targetcleavage activity comparable to that of the canonical TALE, butdrastically reduced cleavage of OffA17 (˜0.3% compared to 6.3% for thecanonical TALE) (FIG. 19A). The effect of the C-terminal Q745Psubstitution, corresponding to Q711P in the CBX8-TALE, was assayed inisolation by site-directed mutagenesis and determined that this mutationdid not effect on-target or off-target cleavage activity in vitro (FIG.19B). The dynamic range of the gel-based in vitro TALEN cleavage assaywas insufficient to distinguish between the specificity enhancement oftwo clones containing identical genotypes differing only by the presence(L3-2) or absence (L3-1) of L338S (FIG. 3B). Collectively, these resultsidentify A252T as a key mutation and L338S as a potential accessorymutation that alter the on-target:off-target cleavage propensity of theATM-targeting TALE (FIGS. 3 and 19A-19D).

To investigate whether the evolved specificity enhancements are limitedto the OffA17 off-target sequence, or if instead they also improve DNAcleavage specificity against other sequences, the ability of the evolvedTALENs to cleave variants of OffA17 was assayed containing subsets ofits five mutations. Cleavage of these sequences was similar between thecanonical and evolved L3-1 TALEN pairs (FIG. 19E). To reveal the broadDNA cleavage specificity of the evolved TALENs, our previously describedTALEN specificity profiling method³⁰ was used to measure the ability ofa TALEN to cleave any of >10¹² DNA sequences that are related to theon-target site. A DNA library was digested that was sufficiently diverseto contain at least ten copies of all DNA sequences with six or fewermutations from the on-target ATM sequence with either the canonicalTALEN pair, or with TALEN pairs containing an evolved ATM-L TALE (L2-1,L3-1, or L3-2) in combination with the canonical ATM-R TALE (see Table 3for statistics). The specificity profile was generated as previouslydescribed³⁰. Next, we calculated the enrichment factor for each librarymember that survived selection by dividing its abundance after selectionby its abundance before selection. Mean enrichment values for theon-target sequence ranged from −8 to 20 across the various samples (FIG.20A, 20B). Importantly, TALEN pairs containing the evolved TALEs L3-1and L3-2 showed a substantially decreased ability to cleave off-targetsequences containing four to nine mutations relative to the canonicalTALEN (FIG. 20B). For example, L3-1 cleaved off-target sequencescontaining seven mutations ˜7-fold less efficiently than the canonicalTALEN (both at 2.5 nM), despite cleaving on-target sequences 2-fold moreefficiently (FIG. 20B). These results indicate that the evolved TALEsexhibit general improvements in specificity that are not limited to theOffA17 off-target site used during negative selection PACE, but insteadincrease the ability of the evolved TALEs to reject other relatedoff-target sequences as well (FIG. 20).

TABLE 3 Statistics of sequences selected by TALEN digestion. Statisticsare shown for the pre-selection library and for DNA surviving each TALENselection on the ATM target sequence. Seq. Mean Stdev Selection countmut. mut. P-value vs. library^(a) Canonical 20 nM 181361 3.991 1.4214.78 × 10⁻¹¹ Canonical 10 nM 180277 3.853 1.396 3.83 × 10⁻¹¹ Canonical 5nM 206958 3.662 1.367 2.40 × 10⁻¹¹ Canonical 2.5 nM 343423 3.282 1.3218.42 × 10⁻¹² L3-1 20 nM 137886 3.617 1.343 3.69 × 10⁻¹¹ L3-1 10 nM141679 3.445 1.318 2.73 × 10⁻¹¹ L3-1 5 nM 190497 3.247 1.297 1.42 ×10⁻¹¹ L3-1 2.5 nM 342976 2.914 1.264 5.20 × 10⁻¹² L3-2 10 nM 1872543.126 1.299 1.22 × 10⁻¹¹ L2-1 10 nM 181692 3.67 1.35 2.83 × 10⁻¹¹Pre-selection library 453246 6.811 2.311 NA Seq. counts: total counts ofhigh-throughput sequenced and computationally filtered selectionsequences. Mean mut.: mean mutations in selected sequences. Stdev. mut.:standard deviation of mutations in selected sequences. Stdev. mut.:standard deviation of mutations in selected sequences. ^(a)Comparisonsbetween the TALEN selection sequence distributions and the correspondingpre-selection library sequence distribution were determined aspreviously reported⁴⁴ using a one-sided t-test.

Specificity scores were calculated to directly compare the preference ofcanonical and evolved ATM-L TALEs at each position in the TALEN targetsite for A, C, G, or T. Scores were calculated by subtracting pre- andpost-selection base-pair frequencies, and normalizing values to themaximum possible change of the pre-selection frequency from perfectspecificity (1.0) to complete lack of specificity (−1.0). Heat maps andquantitative bar graphs generated for the canonical TALEN pair were inagreement with previously reported observations³⁰ (FIGS. 4A, 21, 22).Cleavage by TALEN pairs incorporating the evolved TALEs L3-1 or L3-2exhibited substantially increased specificity relative to that of thecanonical TALEN at nearly all positions in the left half-site of the ATMbinding sequence, but no substantial change in specificity in the righthalf-site that was not used during DB-PACE (FIGS. 4B-4D, 23, 24, 25, and26). Taken together, these results demonstrate that DB-PACE can be usedto greatly reduce TALEN cleavage of a specific genomic off-targetsequence, and that the resulting specificity enhancements are notconfined to that off-target substrate but instead apply to many otheroff-target sequences.

The behavior of the evolved TALENs in two human cell lines was tested.U2OS cells were nucleofected with a control plasmid, or plasmidsexpressing heterodimeric FokI fusions to either the canonical ATM-L TALEor evolved L3-1 or L3-2 TALEs, together with a plasmid encoding thecanonical ATM-R TALE-FokI fusion protein. After 48 h, genomic DNA washarvested and high-throughput sequencing analysis was performed toexamine cleavage at the on-target site, off-target site OffA17, andthree additional unrelated off-target sites OffA1, OffA11, and OffA23³⁰.Cleavage at the on-target ATM site was comparable for the canonical andevolved TALENs (Tables 1, 2, and 4). Importantly, for all fouroff-target sites, both evolved TALENs exhibited reduced off-targetactivity relative to the canonical TALEN (Tables 1 and 4). For example,cleavage of OffA17 was reduced by >16-fold (Tables 1 and 4), andcleavage of OffA11 was reduced by >20-fold (Tables 1 and 4) using eitherthe L3-1 or L3-2 TALENs in human cells versus the canonical TALEN.Comparable on-target activity and improved specificity of the L3-2 TALENagainst the two most efficiently cleaved off-target sites, OffA17 andOffA11, using a homodimeric FokI nuclease architecture in HEK 293 cells(Tables 1 and 4). These data establish that DB-PACE can be used toimprove the specificity of a DNA-binding domain. Moreover, the resultsdemonstrate that the mutations that confer improved specificity duringDB-PACE selection can be applied to other TALE effector contexts, suchas incorporation into a TALEN pair for genome modification in humancells with improved DNA specificity.

TABLE 1 Cellular modification rates of the on-target ATM locus and fouroff-target sites by canonical and evolved TALENs in human U2OS and HEK293 cells. Canonical L3-1 L3-2 Site TALEN(%) TALEN (%) TALEN (%) U2OSOn-target {ATM locus) 11.00 7.040 7.970 OffA1 0.009 <0.001 0.002 OffA110.040 0.002 0.002 OffA17 0.017 <0.001 <0.001 OffA23 0.004 <0.001 <0.001293 On-target {ATM locus) 23.74 ND 23.26 OffA11 0.748 ND <0.001 OffA170.380 ND 0.025

Cellular modification rates are shown as a percentage based on thenumber of observed sequences containing insertions or deletions (indels)divided by the total number of genomic DNA fragments sequenced. Fulltarget sites are listed in Table 2, and total sample sizes and P-valuesare shown in Table 4. ND: no data were collected.

Heterodimeric FokI nuclease (EL/KK) TALENs were used for experiments inU2OS cells, while homodimeric FokI nuclease TALENs were used forexperiments in HEK 293 cells.

TABLE 4 Sample size and P value for high-throughput sequencing of TALENcleavage in U2OS and 293 cells. TALEN Total Percent Cell line pair SiteIndels sequences modified^(a) P-value^(b) U2OS Control On-target 1 100000.010 U2OS Control OffA1 0 253702 <0.001 U2OS Control OffA11 5 4216330.001 U2OS Control OffA17 2 438269 <0.001 U2OS Control OffA23 2 2812880.001 U2OS ATM can. On-target 1100 10000 11.000 <1.0 × 10⁻³⁰⁰   (EL/KK)U2OS ATM can. OffA1 18 193251 0.009 2.8 × 10⁻⁷  (EL/KK) U2OS ATM can.OffA11 144 357899 0.040 5.7 × 10⁻⁴²  (EL/KK) U2OS ATM can. OffA17 95569336 0.017 4.1 × 10⁻²¹  (EL/KK) U2OS ATM can. OffA23 12 338944 0.0042.8 × 10⁻²  (EL/KK) U2OS L3-1 On-target 704 10000 7.040 1.3 × 10⁻²⁰⁴(EL/KK) U2OS L3-1 OffA1 0 275541 <0.001 (EL/KK) U2OS L3-1 OffA11 5314087 0.002 (EL/KK) U2OS L3-1 OffA17 1 420626 <0.001 (EL/KK) U2OS L3-1OffA23 0 351725 <0.001 (EL/KK) U2OS L3-2 On-target 797 10000 7.970 2.1 ×10⁻²³¹ (EL/KK) U2OS L3-2 OffA1 4 235431 0.002 5.4 × 10⁻²  (EL/KK) U2OSL3-2 OffA11 5 303362 0.002 (EL/KK) U2OS L3-2 OffA17 2 489318 <0.001(EL/KK) U2OS L3-2 OffA23 2 401692 <0.001 (EL/KK) 293 Control On-target74 121714 0.061 293 Control OffA11 1 64667 <0.001 293 Control OffA17 3191726 <0.001 293 ATM can. On-target 23651 99604 23.745 <1.0 × 10⁻³⁰⁰  (Homo) 293 ATM can. OffA11 290 38761 0.748 8.8 × 10⁻¹²² (Homo 293 ATMcan. OffA17 639 168318 0.380 1.2 × 10⁻²⁰⁴ (Homo) 293 L3-2 On-target20944 90030 23.263 <1.0 × 10⁻³⁰⁰   (Homo) 293 L3-2 OffA11 0 52317 <0.001(Homo) ^(a)As previously described⁵⁶, the sensitivity of thehigh-throughput sequencing method for detecting genomic off-targetcleavage is limited by the amount genomic DNA (gDNA) input into the PCRamplification of each genomic target site. Each sample was run with 600ng of genomic DNA, equivalent to ~198,000 genomes. Thus, the theoreticaldetection limit of this technique is approximately 1 in 198,000, whichhas been indicated as <0.001%. ^(b)P values were calculated aspreviously reported^(30,44) using a (right) one-sided Fisher's exacttest between each TALEN-treated sample and the untreated control sample.P values less than the significance threshold, calculated as previouslydescribed³⁰, are not shown. Indels are the number of observed sequencescontaining insertions or deletions consistent with TALEN-inducedcleavage, and percent modified corresponds to the number of detectedsequences containing indels divided by the total number of genomic DNAfragments sequenced multiplied by one hundred.

DISCUSSION

DNA-binding PACE brings the power of continuous evolution to bear onimproving the activity and specificity of a variety of DNA-bindingproteins, including those relevant to genome editing (in this work, zincfingers and TALE proteins). A distinguishing feature of DB-PACE is thatit does not require the use of targeted libraries that can constrain orbias evolutionary outcomes. As evidenced by the findings of this study,the unconstrained manner in which mutations arise during PACE supportsthe discovery of evolved solutions with desired properties that couldnot be rationalized a priori. For example, while two directed evolutionstudies using combinatorial libraries^(28,29) have supported theoriginal notion that TALE specificity at the 5′ position is mediatedexclusively by W120 (W232 in AvrBs3 structure⁴⁸), the results identifyK59 and A79 as two residues that also determine 5′ nucleotidespecificity.

A small cluster of mutations (K59E, A79E, and A133E) arising during5′-nucleotide-directed evolution were discovered that are predicted tobe within an extended N-terminal DNA-binding region⁴⁹ near W120.Mutation of A79 or K59 to glutamate resulted in altered 5′ specificity(FIGS. 13D and 16C, 16D). While these residues are not predicted todirectly contact DNA (FIGS. 13C and 16A), their effects are likelymediated through their interactions with W120, which is predicted tocontact the 5′ nucleotide⁴⁹. Moreover, DB-PACE to alter 5′ nucleotidetargeting identified a large number of additional amino acidsubstitutions throughout the entire TALE sequence, and identifiedcontext-dependent effects for residues such as K59E that alter 5′specificity in a non-modular fashion (FIG. 16D). The results thereforesupport the more recent hypothesis that 5′ base specificity is alteredin a complex fashion that depends on the context of TALE repeats andtheir RVD compositions⁵⁰⁻⁵². The findings also suggest that TALEproteins with the most desirable properties, including high activity andhigh specificity, may contain mutations such as K59E that are notentirely modular but rather specific to the TALE protein of interest.Because such mutations are difficult or impossible to predict usingstandard TALE design principles, DB-PACE may be an ideal method toimprove TALE arrays designed by modular assembly.

The data also support recent observations that TALE activity can bealtered in an effector-dependent manner⁵². Mutation of Q711 (orequivalent), was present in an unstructured area of the C-terminus (FIG.13E), to Pro in all PACE experiments performed. While this substitutiondoubled the activity of TALE-ω fusions (FIG. 13B), likely throughintroduction of a kink in protein backbone that resulted in moreeffective presentation of the co RNAP subunit, it had no effect on TALENactivity (FIG. 19B).

The high efficiency of PACE facilitates the accumulation of manypermissive amino acid substitutions in evolving proteins. The resultsshown in FIG. 13A reveal novel sequence variability within the normallyhighly conserved core TALE unit. Of particular note are substitutionsD4K/N and S11K within the first helix¹⁶, and K16R, T21A, and L26F in thesecond helix¹⁶, all of which arose in multiple evolution experiments,and in some cases, in multiple different TALE array repeats (FIG. 12).Position K16, as illustrated in the context of a K634R mutation in FIG.13H, is adjacent to the RVD loop and makes a non-specific DNA contact¹⁶.These results suggest that Arg may be used as a possible alternative atposition 16 for this DNA contact. In addition, it was observed thatseveral RVD substitutions, including replacement of the less specific NNRVD, which targets both G and A¹³, with the more specific NK and NHrepeats¹⁷, as well as substitution of NG with HG, a repeat present innaturally occurring TALEs that also specifies T, but is not typicallyused in the design of synthetic TALEs (FIG. 13A)¹⁷. It has been shownthat the highly repetitive nature of TALEN genes is incompatible withlentiviral delivery vectors due to recombination between repeat unitsarising from “template-switching” during DNA replication⁵³. Thepermissive core amino acid substitutions discovered in this work couldenable recoding of TALE arrays to decrease sequence homology and therebyimprove the manipulability and application scope of TALE proteins.

The data demonstrate that DB-PACE coupled with in vitro specificityprofiling represents a systematic approach to removing specificoff-target activities of TALENs. In theory, negative selection againstbinding to a particular TALE off-target site could result in theemergence of a new off-target activity. However, our broad specificityprofiling data suggest that TALEs may possess an inherent degree ofpromiscuity, possibly arising from excess DNA-binding energy³⁰, that canbe decreased through rapid protein evolution to improve TALE arrayspecificity in a broad manner. It is tempting to speculate that TALEsfrom Xanthomonas may have evolved a degree of promiscuity to enable themto target slightly mutated pathogen sequences inside a plant host, ahypothesis supported by the recent identification of naturally occurringTALEs with the ability to bind target sequence variants with singlenucleotide deletions⁵⁴. It is remarkable that a single amino acidsubstitution, A252T, corresponding to the eighth residue within thethird repeat of the ATM-L TALE, can greatly diminish binding of theOffA17 off-target site, which contains mutations at target sitenucleotides 1, 5, 12, 16, and 17. Structural analysis predicts that A252lies in close proximity to the RVD loop (FIG. 19C), and it has beensuggested that this residue stabilizes the loop^(15,16,55). It isplausible that mutation of this residue to a larger and more polar Thrresidue results in an altered or additional DNA contact, alteringspecificity of the entire array. The fact that evolved ATM-L TALE L3-2showed even greater specificity than L3-1 (FIGS. 26A, 26B) and differedonly by the presence of L338S suggests that this position is also adeterminant of specificity. L338, which corresponds to position 26 in aTALE repeat, is adjacent to P339 (FIG. 19D), a residue that is essentialfor proper packing of TALE repeats¹⁶. L338S may adjust repeat packing ina way that decreases excess binding energy and thereby augmentsspecificity.

The development of DB-PACE may facilitate the generation of highlyspecific genome engineering tools for research or therapeuticapplications. For example, DB-PACE could be used to evolve high-affinitymatched TALE pairs for accurate SNP detection. Moreover, DB-PACE isamenable to improving the specificity of TALENs targeting loci ofclinical relevance such as CCR5³⁰ (FIG. 27), as well as improving othergenome engineering tools with clinical potential such as Cas9.Accordingly, DB-PACE could be used to remove the undesirable ability ofthese proteins to modify specific off-target loci, thereby increasingtheir safety and therapeutic potential.

Materials and Methods

Cloning and Plasmid Construction.

PCR fragments for pOH, pAP, pAPNeg, pJG, and SP plasmids were generatedusing either PfuTurbo Cx Hotstart (Agilent) or VeraSeq Ultra(Enzymatics) DNA polymerases, and assembled by USER cloning (NEB)according to the manufacturer's instructions. The Q5 Site-DirectedMutagenesis kit (NEB) was used for all site-directed mutagenesis, and toproduce minimized pOH plasmids (pTet). DNA encoding TALEN cleavage siteswere purchased as gBlocks (IDT) and inserted into pUC19 using XbaI andHindIII restriction enzymes.

Phage-Assisted Continuous Evolution (PACE) of DNA-Binding Domains.

In general, PACE setup was performed as previously described³³ . E. coliwere maintained in chemostats containing 200 mL of Davis' Rich Media(DRM) using typical flow rates of 1-1.5 vol/h. DRM media wassupplemented with appropriate antibiotics to select for transformedplasmids: APs (50 μg/mL carbenicillin), APNegs (75 μg/mL spectinomycin),MPs (25 μg/mL chloramphenicol). Lagoon dilution rates were 1.3-2 vol/h.In all PACE experiments S1030 cells carried an MP, either the previouslyreported pJC 184³³, or a variant of this plasmid lacking RecA, pAB086a.Mutagenesis was induced by continuously injecting arabinose (500 mM) ata rate of 1 mL/h into each 40-mL lagoon. Typical phage titers duringeach PACE experiment were 10⁶-10⁸ p.f.u./mL. Specific parameters foreach evolution experiment are detailed below.

Reversion of Zif268-V24R.

A lagoon receiving host cell culture from a chemostat containing S1059cells transformed with an MP was inoculated with Zif268-V24R phage. Thelagoon flow rate during drift was 2 vol/h. After 24 h of drift, phagewere isolated and used to inoculate a PACE experiment with S1030 hostcells carrying pAPZif268 and an MP. Evolved phage were isolated after 24h and characterized using plaque assays.

Positive Selection of TALEs with Altered 5 ′ Preference (5′A, C, G).

Three parallel evolution experiments were performed to evolve phage withhigher affinity for 5′ A, 5′ C, or 5′ G target sequences. For eachexperiment, two separate lagoons receiving culture from a chemostatcontaining S1030 cells transformed with the appropriate AP(pAPCBXTAL:5A, pAPCBXTAL:5C, pAPCBXTAL:5G) and an MP were inoculatedwith SPCBXTAL. PACE proceeded for 48 h at a lagoon dilution rate of 1.3vol/h prior to harvest and analysis of the resultant phage pools.

Negative Selection to Generate TALEs with 5′ A Specificity.

Two separate lagoons receiving culture from a chemostat containing amixed population of S1030 cells were inoculated with evolved 5′ A phagefrom the positive selection experiment. This E. coli populationconsisted of a 1:1:1 mixture of host cells carrying an APNeg plasmid(pAPNegCBXTAL:5C, pAPNegCBXTAL:5G, or pAPNegCBXTAL:5T) together withpAPCBXTAL:5A and an MP. Over the course of a six-day PACE experiment, anincreasing dose of theophylline was added to each lagoon at a rate of 1mL/h to yield increasing final theophylline lagoon concentrations of 0.1mM, 0.2 mM, and 0.3 mM (+0.1 mM theophylline every 48 h).

Positive Selection and Negative Selection (OffA17) of ATM-L TALE.

Two separate lagoons receiving culture from a chemostat containing aS1030 cells transformed with pAPATMLTAL, pAPNegATMTAL:OffA17, and an MPwere inoculated with SPATMTAL phage. The lagoon flow rate was 1.3 vol/h.Theophylline was added to each lagoon at increasing quantities (+0.1 mMevery 24 h), from a starting dose of 0 mM to a final concentration of0.4 mM; the injection rate into each lagoon was 1 mL/h. After 120 h ofPACE, phage from both lagoons were pooled and subjected to an additional24 h of PACE at a lagoon flow rate of 2 vol/h in the presence of 0.4 mMtheophylline.

Luciferase Assay.

pOH plasmids were transformed by electroporation into S1030 cells, andgrown overnight at 37° C. on LB-agar plates supplemented with 50 μg/mLcarbenicillin. Single colonies were used to inoculate cultures whichwere allowed to grow for ˜12 h at 37° C. in DRM supplemented with 50μg/mL carbenicillin in a shaker. Cultures were diluted to an OD₆₀₀ of˜0.3 and allowed to grow for an additional 2 h at 37° C. Next, eachculture was diluted 1:15 into 300 μL of DRM supplemented with 50 μg/mLcarbenicillin in the presence or absence of 200 ng/mLanhydrotetracycline and incubated in a 96-well plate for an additional4-6 h (shaking). 200 μL aliquots of each sample were then transferred to96-well opaque plates and luminescence and OD₆₀₀ readings were takenusing a Tecan Infinite Pro instrument. Luminescence data were normalizedto cell density by dividing by the OD₆₀₀ value.

Plaque Assays.

S1030 cells were transformed with the appropriate plasmids viaelectroporation and grown in LB media to an OD₆₀₀ of 0.8-1.0. Dilutedphage stock samples were prepared (10⁴, 10⁵, 10⁶, or 10⁷-fold dilution)by adding purified phage stock to 250 μL of cells in Eppendorf tubes.Next, 750 μL of warm top agar (0.75% agar in LB, maintained at 55° C.until use) was added to each tube. Following mixing by pipette, each 1mL mixture was pipetted onto one quadrant of a quartered petri platethat had previously been prepared with 2 mL of bottom agar (1.5% agar inLB). Following solidification of the top agar, plates were incubatedovernight at 37° C. prior to analysis. Colorimetric plaque assays wereperformed in parallel with regular plaque assays using S2060 cellsinstead of S1030 cells, and used S-Gal/LB agar blend (Sigma) in place ofregular LB-agar.

High-Throughput Analysis of TALE Mutations.

PCR fragments containing evolved phage with −500 bp of flanking sequenceon either end were amplified from minipreps (Qiagen) of cells infectedwith evolved phage pools using the following primers:HTSFwd-5′-GAAAATATTGTTGATGCGCTGGCAGTGTTC-′3 (SEQ ID NO: 46),HTSRev-5′-TAGCAGCCTTTACAGAGAGAATAACATAAAA-′3 (SEQ ID NO: 47). HTSpreparation was performed as previously reported using a Nextera kit(Illumina). Briefly, 4 μL of amplified DNA (2.5 ng/μL), 5 μL TD buffer,and 1 μL TDE1 were mixed together and heated at 55° C. for 5 min toperform “tagmentation”. Following DNA clean up using a Zymo-Spin column(Zymo), samples were amplified with Illumina-supplied primers accordingto the manufacturer's instructions. The resulting products were purifiedusing AMPure XP beads (Agencourt), and the final concentration of DNAwas quantified by qPCR using PicoGreen (Invitrogen). Samples weresequenced on a MiSeq Sequencer (Illumina) using 2×150 paired-end runsaccording to the manufacturer's protocols. Analysis of mutationfrequency was performed using MATLAB as previously described³². Observedbackground mutation frequencies were subtracted from the mutationfrequencies of each experimental sample to account for DNA sequencingerrors³².

YFP Assay.

pTet plasmids were co-transformed with pAPNeg plasmids byelectroporation into S1030 cells, and grown overnight at 37° C. onLB-agar plates supplemented with 50 μg/mL carbenicillin and 100 μg/mLspectinomycin. Single colonies were used to inoculate cultures whichwere allowed to grow for ˜12 h in antibiotic-supplemented DRM in abacterial shaker. Cultures were diluted to an OD₆₀₀ of ˜0.3 and allowedto grow for an additional 2 h at 37° C. Next, each culture was diluted1:15 into 300 μL of DRM supplemented with antibiotics and 5 mMtheophylline in the presence or absence of 50 ng/mL anhydrotetracyclineand incubated in a 96-well deep well plate for an additional 4-6 h(shaking). 200 μL aliquots of each sample were then transferred to96-well opaque plates and YFP fluorescence (λ_(ex)=514 nm, λ_(em)=527nm) and OD₆₀₀ readings were taken using a Tecan Infinite Pro instrument.Fluorescence data were normalized to cell density by dividing by theOD₆₀₀ value.

In Vitro TALEN Cleavage Assay.

In vitro TALEN cleavage assays were performed as previously describedwith slight modifications to the procedure³⁰. Briefly, 1 g of eachTALEN-encoding plasmid (pJG) was added individually to 20 μL ofmethionine-supplemented T7-TnT Coupled Transcription/Translation System(Promega) lysate and incubated for 1.5 h at 30° C. Determination ofprotein concentrations and preparation of linear DNA for TALEN cleavagewas performed as previously reported³⁰ Each reaction consisted of 50 ngof amplified DNA, 12 μL NEB Buffer 3, 3 μL of each in vitrotranscribed/translated TALEN left and right monomers (corresponding to−15 nM final TALEN concentration), and 6 μL of empty lysate brought upto a final volume of 120 μL in distilled water. The digestion reactionwas allowed to proceed for 30 min at 37° C. (or 1 h where indicated),and then incubated with 1 μg/uL RNase A (Qiagen) for 2 minutes prior tobeing purified using a Minielute column (Qiagen). Reactions weresubsequently run in a 5% TBE Criterion PAGE gel (Bio-rad), and stainedwith 1×SYBR Gold (Invitrogen) for 10 minutes. Gels were imaged using aSyngene G:BOX Chemi XRQ, and densitometry was performed using GelEval1.37 software.

High-Throughput Specificity Profiling Assay.

High-throughput specificity profiling of canonical and evolved TALENpairs and subsequent data analysis was performed as previouslydescribed³⁰.

TALEN Cleavage in HEK 293 and U20S Cells.

pJG29 and pJG30 plasmids were transfected into HEK 293 cells (a cellline that has a high transfection efficiency; obtained from ATCC) usingLipoject (Signagen) according to the manufacturer's instructions. pJG51and pJG52 plasmids were nucleofected into U20S cells as previouslydescribed³⁰. For both sets of experiments, genomic DNA isolation wasperformed as previously reported^(30,56). Primers for amplifying on andoff-target genomic sites are provided herein. Illumina adapter ligation,AMPure XP bead cleanup (Agencourt), sequencing and post-analysis wereperformed as previously described^(30, 56.)

Plasmid Construct Information

Antibio. Origin of Binding Name Class Res. Rep. Promoter Site GenepOHZif268-1 One- Carb SC101 P_(lac)(pIII- -55(Zif268) pIII-luxABhybrid test luc)P_(tet) Zif268 DBD plasmid (Zif268 (M)-rpoZ fusion)pOHZif268-2 One- Carb SC101 P_(lac)(pIII-luc) -55(Zif268) pIII-luxABhybrid test P_(tet) Zif268 DBD- plasmid (Zif268 (L)-rpoZ fusion)pOHZif268-3 One- Carb SC101 P_(lac)(pIII- -62(Zif268) pIII-luxABhybrid test luc)P_(tet) Zif268 DBD plasmid (Zif268 (M)-rpoZ fusion)pOHZif268-4 One- Carb SC101 P_(lac)(pIII- -62(Zif268) pIII-luxABhybrid test luc)P_(tet) Zif268 DBD plasmid (Zif268 (L)-rpoZ fusion)pOHZif268-5 One- Carb SC101 P_(lac)(pIII- -55(Zif268) pIII-luxABhybrid test luc)P_(tet) rpoZ-(M)-Zif268 plasmid (Zif268 DBD fusion)pOHZif268-6 One- Carb SC101 P_(lac)(pIII- -55(Zif268) pIII-luxABhybrid test luc)P_(tet) rpoZ-(L)-Zif268 plasmid (Zif268 DBD fusion)pOHZif268-7 One- Carb SC101 P_(lac)(pIII- -62(Zif268) pIII-luxABhybrid test luc)P_(tet) rpoZ-(M)-Zif268 plasmid (Zif268 DBD fusion)pOHZif268-7: One- Carb SC101 P_(lac)(pIII- -62 pIII-luxAB TTAhybrid test luc)P_(tet) 5′GCGTTA rpoZ-(M)-Zif268 plasmid (Zif268 GCG3′DBD fusion) pOHZif268-8 One- Carb SC101 P_(lac)(pIII- -62(Zif268)pIII-luxAB hybrid test luc)P_(tet) rpoZ-(L)-Zif268 plasmid (Zif268 DBDfusion) pOHZif268-9 One- Carb SC101 P_(lac)(pIII- -55(Zif268) pIII-luxABhybrid test luc)P_(tet) rpoA-(M)-Zif268 plasmid (Zif268 DBD fusion)pOHZif268-10 One- Carb SC101 P_(lac)(pIII- -62(Zif268) pIII-luxABhybrid test luc)P_(tet) rpoA-(M)-Zif268 plasmid (Zif268 DBD fusion)SPZif268 SP Kan F1 P_(gIII) — rpoZ-(M)- Zif268 DBD SPZif268- SP Kan F1P_(gIII) — rpoZ-(M)- R24V Zif268 DBD- R24V pAPZif268 AP Carb SC101P_(lac) -62(Zif268) pIII-luxAB pAPZif268: AP Carb SC101 P_(lac) -62pIII-luxAB TTA 5′GCGTTA GCG3′ pOHCBXTAL-1 One-hybrid Carb SC101Plac(pIII-luc) -62(CBX8) pIII-luxAB test Ptet(CBX8 TALE(CBX8)- plasmidTALE fusion) +28-rpoZ pOHCBXTAL-2 One-hybrid Carb SC101 Plac(pIII-luc)-62(CBX8) pIII-luxAB test Ptet(CBX8 TALE(CBX8)- plasmid TALE fusion)+40-rpoZ pOHCBXTAL-3 One-hybrid Carb SC101 Plac(pIII-luc) -62(CBX8)pIII-luxAB test Ptet(CBX8 TALE(CBX8)- plasmid TALE fusion) +63-rpoZpOHCBXTAL-4 One- Carb SC101 P_(lac)(pIII-luc) -62(CBX8) pIII-luxABhybrid test P_(tet)(CBX8 TALE(CBX8)-  plasmid TALE fusion) +18G₄S-rpoZpOHCBXTAL-4: One- Carb SC101 P_(lac)(pIII-luc) -62 5′ pIII-luxABOfftarget hybrid test P_(tet)(CBX8 TTCATAA TALE(CBX8)- plasmidTALE fusion) GGGATTA +18G₄S-rpoZ GGC3′ pOHCBXTAL-4: One- Carb SC101P_(lac)(pIII-luc) -62(CBX8) pIII-luxAB A79E, A133E, hybrid testP_(tet)(CBX8 TALE(CBX8)- Q711P, A755V plasmid TALE fusion) +18G₄S-rpoZV767G pOHCBXTAL-4: One- Carb SC101 P_(lac)(pIII-luc) -62 pIII-luxAB5A,L1-1..5, hybrid test P_(tet)(CBX8 5′ATCAGG TALE(CBX8)- L2-1..5, A79E,plasmid TALE fusion) AGGGCTT +18G₄S-rpoZ K59E CGGC 3′ pOHCBXTAL- One-Carb SC101 P_(lac)(pIII-luc) -62 pIII-luxAB 4:5C,L1-1..5, hybrid testP_(tet)(CBX8 5′CTCAGG TALE(CBX8)- L2-1..5, A79E, plasmid TALE fusion)AGGGCTT +18G₄S-rpoZ K59E CGGC 3′ pOHCBXTAL-4: One- Carb SC101P_(lac)(pIII-luc) -62 pIII-luxAB 5G, L1-1..5, hybrid test P_(tet)(CBX85′GTCAGG TALE(CBX8)- L2-1..5, A79E, plasmid TALE fusion) AGGGCTT+18G₄S-rpoZ K59E CGGC3′ pOHCBXTAL-5 One- Carb SC101 P_(lac)(pIII-luc)-62(CBX8) pIII-luxAB hybrid test P_(tet)(CBX8 TALE(CBX8)- plasmidTALE fusion) +28G₄S-rpoZ SPCBXTAL SP Kan Fl P_(gIII) — TALE(CBX8)+18G₄S-rpoZ pApCBXTAL AP Carb SC101 P_(lac) -62(CBX8) pIII-luxABpApCBXTAL: AP Carb SC101 P_(lac) -62 pIII-luxAB 5A 5′ATCAGG AGGGCTTCGGC 3′ pApCBXTAL: AP Carb SC101 P_(lac) -62 pIII-luxAB 5C 5′CTCAGGAGGGCTT CGGC 3′ pApCBXTAL: AP Carb SC101 P_(lac) -62 pIII-luxAB 5G5′GTCAGG AGGGCTT CGGC 3′ pAPCBXTAL: AP Carb SC101 P_(lac) -62 5′pIII-luxAB Offtarget TTCATAA GGGATTA GGC3′ pAPNegCBXTAL: AP-neg SpectColE1 P_(lac) -62 TheoRibo- 5A 5′ATCAGG 6xHistag-N- AGGGCTT C83-VenusCGGC 3′ pAPNegCBXTAL: AP-neg Spect ColE1 P_(lac) -62 TheoRibo- 5C5′CTCAGG 6xHistag-N- AGGGCTT C83-Venus CGGC 3′ pAPNegCBXTAL: AP-negSpect ColE1 P_(lac) -62 TheoRibo- 5G 5′GTCAGG 6xHistag-N- AGGGCTTC83-Venus CGGC 3′ pAPNegCBXTAL: AP-neg Spect ColE1 P_(lac) -62 TheoRibo-5T 5′TTCAGG 6xHistag-N- AGGGCTT C83-Venus CGGC 3′ pAPNegCBXTAL: AP-negSpect ColE1 P_(lac) -62 5′ TheoRibo- Offtarget TTCATAA 6xHistag-N-GGGATTA C83-Venus GGC 3′ pTetCBXTAL Inducible Carb SC101 P_(tet)(CBX8 —TALE(CBX8)- TALE TALE fusion) +18G₄S-rpoZ express. pTetCBXTAL: InducibleCarb SC101 P_(tet)(CBX8 — TALE(CBX8)- L1-1, L1-2, TALE TALE fusion)+18G₄S-rpoZ L2-1, L2-2 express. SPATMTAL SP Kan F1 P_(gIII) —TALE(ATM-L) +18G4S-rpoZ pApATMTAL AP Carb SC101 P_(lac) -62(ATM-L)pIII-luxAB pAPNegATMTAL: AP-neg Spect ColE1 P_(lac) -62 5′- TheoRibo-OffA17 GAAATGG 6xHistag-N- GATACTG C83-Venus AGT3′ pUC19-On- TALEN CarbpMB1 — Cleavage — target cleavage site: ATM-L pUC19-Off- TALEN Carb pMB1— Cleavage — target, pUC19- cleavage site: 5′- OffD1-D4 GAAATGG GATACTGAGT3′ or derivative site pOHATMTAL One- Carb SC101 P_(lac)(pIII-luc) -62TALE(ATM-L)- hybrid test P_(tet) (ATM-L) +18G₄S-rpoZ plasmid(TALE fusion) pOHATMTAL: One- Carb SC101 P_(lac)(pIII- -62 TALE(ATM-L)-L3-1, L3-2 hybrid test luc)P_(tet) (ATM-L) +18G₄S-rpoZ plasmid(TALE fusion) pOHATMTAL: One- Carb SC101 P_(lac)(pIII- -62 TALE(ATM-L)-OffA17 hybrid test luc)P_(tet) 5′- +18G₄S-rpoZ plasmid (TALE fusion)GAAATGG GATACTG AGT3′ pOHATMTAL: One- Carb SC101 _(Plac)(pIII- -62TALE(ATM-L)- OffA17:L3-1, hybrid test luc)P_(tet) 5′- +18G₄S-rpoZ L3-2plasmid (TALE fusion) GAAATGG GATACTG AGT3′ pOHATMTAL: One- Carb SC101P_(lac)(pIII- -62 TALE(ATM-L 5′A,C,G and hybrid test luc)P_(tet)(ATM-L) or or K59E mut)- K59E- plasmid (TALE 5′A,C,G +18G₄S-rpoZ5′A,C,G,T fusion) sequence variant pOHCCR5TAL, One- Carb SC101P_(lac)(pIII- 5′- TALE(CCR5-R)- pOHCCR5TAL: hybrid test luc)P_(tet)TCTTCCA +18G₄S- Off5, Off15, plasmid (TALE GAATTGA rpoZ Off28 fusion)TACT-′3 or off-target site pAB086a MP Chlor RecA-version of pJC184³³pJG29:L1-1, Backbone information previously described³⁰ L1-2, L2-1, L3-1..L3-4, Q745P pJG30 Backbone information previously described³⁰pJG51: L3-2 Backbone information previously described³⁰ pJG52Backbone information previously described³⁰

Genotypes of Bacterial Strains

Strain Genotype S1030 F′ proA+B+ Δ(lacIZY) zzf::Tn10 lacIQ1 PN25-tetRluxCDE/endA1 recA1 galE15 galK16 nupG rpsL ΔlacIZYA araD139 Δ(ara,leu)7697 mcrA Δ(mrr-hsdRMS-mcrBC) proBA::pir116 araE201 ΔrpoZ ΔfluΔcsgABCDEFG ΔpgaC λ− S1059 F′ proA+B+ Δ(lacIZY) zzf::Tn10 lacIQ1PN25-tetR luxCDE/endA1 recA1 galE15 galK16 nupG rpsL ΔlacIZYA araD139Δ(ara, leu)7697 mcrA Δ(mrr-hsdRMS-mcrBC) proBA::pir116 araE201 ΔrpoZ λ−pJC175e³³ S1632 F′ proA+B+ Δ(lacIZY) zzf::Tn10 lacIQ1 PN25-tetRluxCDE/endA1 recA1 galE15 galK16 nupG rpsL ΔlacIZYA araD139 Δ(ara,leu)7697 mcrA Δ(mrr-hsdRMS-mcrBC) proBA::pir116 araE201 ΔrpoZ ΔfluΔcsgABCDEFG ΔpgaC ΔpspBC λ− S2058 F′ proA+B+ Δ(lacIZY) zzf::Tn10 lacIQ1PN25-tetR luxCDE Ppsp lacZ luxR Plux groESL/endA1 recA1 galE15 galK16nupG rpsL ΔlacIZYA araD139 Δ(ara, leu)7697 mcrA Δ(mrr-hsdRMS-mcrBC)proBA::pir116 araE201 ΔrpoZ Δflu ΔcsgABCDEFG ΔpgaC λ− S2059 F′ proA+B+Δ(lacIZY) zzf::Tn10 lacIQ1 PN25-tetR luxCDE Ppsp(T1) lacZ luxR PluxgroESL/endA1 recA1 galE15 galK16 nupG rpsL ΔlacIZYA araD139 Δ(ara,leu)7697 mcrA Δ(mrr-hsdRMS-mcrBC) proBA::pir116 araE201 ΔrpoZ ΔfluΔcsgABCDEFG ΔpgaC λ− S2060 F′ proA+B+ Δ(lacIZY) zzf::Tn10 lacIQ1PN25-tetR luxCDE Ppsp(AR2) lacZ luxR Plux groESL/endA1 recA1 galE15galK16 nupG rpsL ΔlacIZYA araD139 Δ(ara, leu)7697 mcrAΔ(mrr-hsdRMS-mcrBC) proBA::pir116 araE201 ΔrpoZ Δflu ΔcsgABCDEFG ΔpgaCλ− S2208 F′ proA+B+ Δ(lacIZY) zzf::Tn10 lacIQ1 PN25-tetR luxCDEPpsp(AR2) lacZ luxR Plux groESL/endA1 recA1 galE15 galK16 nupG rpsLΔlacIZYA araD139 Δ(ara, leu)7697 mcrA Δ(mrr-hsdRMS-mcrBC) proBA::pir116araE201 ΔrpoZ Δflu ΔcsgABCDEFG ΔpgaC λ− pJC175e³³

Primer Sequences Used to Amplify On- and Off-Target ATM Genomic Sites

OnATM F: (SEQ ID NO: 26)5′GGAGTTCAGACGTGTGCTCTTCCGATCTAGCGCCTGATTCGAGATCC T-′3 OnATM R:(SEQ ID NO: 27) 5′-CACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNATGCCAAATTCATATGCAAGGC-′3 OffA-1F: (SEQ ID NO: 28)5′ GGAGTTCAGACGTGTGCTCTTCCGATCTCCTGCCATTGAATTCCAG CCT-′3 OffA-1R:(SEQ ID NO: 29) 5′-CACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNTGTCTGCCTTTCCTGTCCCC-′3 OffA-11F: 5′-GGAGTTCAGACGTGTGCTCTTCCGATCTTGCAGCTACGGATGAAAACCA T-′3 OffA-11R:(SEQ ID NO: 30) 5′-CACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNTCAGAATACCTCCCCGCCAG-′3 OffA-17F: (SEQ ID NO: 31)5′-GGAGTTCAGACGTGTGCTCTTCCGATCTGGTGGAACAATCCACCTG TATTAGC-′3 OffA-17R:(SEQ ID NO: 32) 5′-CACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNGAATGTGACACCACCACCGC-′3 OffA-23F: (SEQ ID NO: 33)5′-GGAGTTCAGACGTGTGCTCTTCCGATCTTGTTTAGTAATTAAGACC CTGGCTTTC-′3 OffA-23R:(SEQ ID NO: 34) 5-′CACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNGCGACAGGTACAAAGCAGTCCAT-′3

DNA Sequence of ω-Zif268-DBD Fusion Protein

Bases 997-1260 of m. musculus Zif268, corresponding the zinc fingerDNA-binding domain (residues 333-420)³⁷, were cloned in downstream ofthe RNAP w subunit. Bases 997-1260 of m. musculus Zif268

(SEQ ID NO: 44) 5′ATGGCACGCGTAACTGTTCAGGACGCTGTAGAGAAAATTGGTAACCGTTTTGACCTGGTACTGGTCGCCGCGCGTCGCGCTCGTCAGATGCAGGTAGGCGGAAAGGATCCGCTGGTACCGGAAGAAAACGATAAAACCACTGTAATCGCGCTGCGCGAAATCGAAGAAGGTCTGATCAACAACCAGATCCTCGACGTTCGCGAACGCCAGGAACAGCAAGAGCAGGAAGCCGCTGAATTACAAGCCGTTACCGCTATTGCTGAAGGTCGTCGTGCGGCGGGCGGCGGCGGCAGCACCGCGGCGGCTGAACGCCCATATGCTTGCCCTGTCGAGTCCTGCGATCGCCGCTTTTCTCGCTCGGATGAGCTTACCCGCCATATCCGCATCCACACAGGCCAGAAGCCCTTCCAGTGTCGAATCTGCATGCGTAACTTCAGTCGTAGTGACCACCTTACCACCCACATCCGCACCCACACAGGCGAGAAGCCTTTTGCCTGTGACATTTGTGGGAGGAAGTTTGCCAGGAGTGATGAACGCAAGAGGCATACCAAAATCCATTTAAGACAGAAGTAA-3′ 

Coding Sequence for w-Zif268-DBD Fusion Protein

The protein sequence of the w-Zif268-DBD fusion protein is shown below.The residues highlighted in bold correspond to the w subunit, while theunderlined correspond to the 11-amino acid linker. Residues shown initalics comprise the Zif268-DBD (residues 333-420)³⁷.ω-Zif268-DBD fusionprotein:

(SEQ ID NO: 45) MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAELQAVTAIAEGRRA AGGGGSTA AAERPYACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFARSDERKRHTKIHLRQK

Coding Sequences for CBX8- and ATM-L-Directed TALE-ω Fusion Proteins

DNA sequences for the CBX8-directed TALE^(18, 20) and the ATM-L directedTALE^(18,20,30) have previously been reported. The protein sequences ofboth TALE-ω fusion proteins are included below, indicating theappropriate residue numbering convention used in this manuscript. Theunformatted residues comprise an N-terminal Flag-tag and NLS sequence,while the bold residues correspond to the canonical N-terminal TALEsequence. TALE repeats are italicized, the C-terminal region and linkersequence underlined, and the w subunit is in bold and italicized. TheDNA and protein sequences for the CCR5-R TALE have also been previouslyreported³⁰. The fusion architecture for the CCR5-R TALE-w protein isidentical to that of the CBX8 and ATM-L-directed TALEs described below.

CBX8-Directed TALE-ω Fusion Protein:

(SEQ ID NO: 11) MDYKDHDGDYKDHDIDYKDDDDKMAPKKKRKVGIHRGVPMVDLRTLGYSQQQQEKIKPKVRSTVAQHHEALVGHGFTHAHIVALSQHPAALGTVAVKYQDMIAALPEATHEAIVGVGKQWSGARALEALLTVAGELRGPPLQLDTGQLLKIAKRGGVTAVEAVHAWRNALTGAPLN LTPDQVVAIASNGGGKQALETVQRLLPVLCQDHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNIGGKQALETVQRLLPVLCQAHGLTPAQWAIANNNGGKQALETVQRLLPVLCQDHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQDHGLTPEQVVAIASNIGGKQALETVQRLLPVLCQAHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPAQVVAIANNNGGKQALETVQRLLPVLCQDHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQDHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPAQVVAIASNGGGKQALETVQRLLPVLCQDHGLTPDQVVAIASHDGGKQALETVQRLLPVLCQDHGLTPEQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPEQWAIAS HDGGRPALESIVAQLSRPDPALAALTNGGGGS

ATM-Directed TALE-ω Fusion Protein.

(SEQ ID NO: 13) MDYKDHDGDYKDHDIDYKDDDDKMAPKKKRKVGIHRGVPMVDLRTLGYSQQQQEKIKPKVRSTVAQHHEALVGHGFTHAHIVALSQHPAALGTVAVKYQDMIAALPEATHEAIVGVGKQWSGARALEALLTVAGELRGPPLQLDTGQLLKIAKRGGVTAVEAVHAWRNALTGAPLN LTPDQVVAIANNNGGKQALETVQRLLPVLCQDHGLTPEQVVAIASNIGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNIGGKQALETVQRLLPVLCQAHGLTPAQWAIASNGGGKQALETVQRLLPVLCQDHGLTPDQVVAIASNGGGKQALETVQRLLPVLCQDHGLTPEQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPAQWAIANNNGGKQALETVQRLLPVLCQDHGLTPDQVVAIASNIGGKQALETVQRLLPVLCQDHGLTPEQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPAQVVAIASHDGGKQALETVQRLLPVLCQDHGLTPDQVVAIASNGGGKQALETVQRLLPVLCQDHGLTPEQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPAQVVAIASNGGGKQALETVQRLLPVLCQDHGLTPEQVVAIASNGGGRPALE SIVAQLS RPDPALAALTNGGGGS

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SEQUENCES

Exemplary Canonical N-Terminal TALE Domain:

(SEQ ID NO: 1) VDLRTLGYSQQQQEKIKPKVRSTVAQHHEALVGHGFTHAHIVALSQHPAALGTVAVKYQDMIAALPEATHEAIVGVGKQWSGARALEALLTVAGELRGPPLQLDTGQLLKIAKRGGVTAVEAVHAWRNALTGAPLN

Generic Formula of a TALE Repeat Sequence:

(SEQ ID NO: 2) LTPX₁QVVAIAX ₂ X ₃X₄GGX₅X₆ALETVQRLLPVLCQX₇HGIn SEQ ID NO: 2, above, X₁ is D, E or A, X₂ is S or N, X₃ is N or H, X₄is G, D, I, or N, X₅ is K or R, X₆ is Q or P, and/or X₇ is D or A.

Exemplary, canonical C-terminal TALE domain:

(SEQ ID NO: 3) SIVAQLSRPDPALAALTNDHLVALACLGGRPALDAVKKGLPHAPALIKRTNRRIPERTSHRVA

Amino acid residues 1-28 of exemplary canonical C-terminal TALE domain:

(SEQ ID NO: 4) SIVAQLSRPDPALAALTNDHLVALACLG

Amino acid residues 1-18 of an exemplary canonical C-terminal TALEdomain:

(SEQ ID NO: 5) SIVAQLSRPDPALAALTN

Exemplary CBX8-Targeting TALE Repeat Array:

(SEQ ID NO: 6) LTPDQVVAIASNGGGKQALETVQRLLPVLCQDHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNIGGKQALETVQRLLPVLCQAHGLTPAQVVAIANNNGGKQALETVQRLLPVLCQDHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQDHGLTPEQVVAIASNIGGKQALETVQRLLPVLCQAHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPAQVVAIANNNGGKQALETVQRLLPVLCQDHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQDHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPAQVVAIASNGGGKQALETVQRLLPVLCQDHGLTPDQVVAIASHDGGKQALETVQRLLPVLCQDHGLTPEQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPEQVVAIASHDGGRPALE 

Exemplary CBX8-targeting TALE (comprising an N-terminal domain, a TALErepeat array and an 18 amino acid C-terminal domain):

(SEQ ID NO: 7) VDLRTLGYSQQQQEKIKPKVRSTVAQHHEALVGHGFTHAHIVALSQHPAALGTVAVKYQDMIAALPEATHEAIVGVGKQWSGARALEALLTVAGELRGPPLQLDTGQLLKIAKRGGVTAVEAVHAWRNALTGAPLNLTPDQVVAIASNGGDGKQALETVQRLLPVLCQHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNIGGKQALETVQRLLPVLCQAHGLTPAQVVAIANNNGGKQALETVQRLLPVLCQDHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQDHGLTPEQVVAIASNIGGKQALETVQRLLPVLCQAHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPAQVVAIANNNGGKQALETVQRLLPVLCQDHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQDHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPAQVVAIASNGGGKQALETVQRLLPVLCQDHGLTPDQVVAIASHDGGKQALETVQRLLPVLCQDHGLTPEQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPEQVVAIASHDGGRPALESIVAQLSRPDPALAALTN 

Exemplary Linker Sequence:

(SEQ ID NO: 8) GGGGS

Exemplary N-Terminal FLAG and NLS:

(SEQ ID NO: 9) MDYKDHDGDYKDHDIDYKDDDDKMAPKKKRKVGIHRGVP

Exemplary RNAP Domain:

(SEQ ID NO: 10) ARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAELQAVTAIAEGRR

Exemplary CBX8-Targeting TALE Construct with FLAG, NLS, and RNAPω:

(SEQ ID NO: 11) MDYKDHDGDYKDHDIDYKDDDDKMAPKKKRKVGIHRGVPMVDLRTLGYSQQQQEKIKPKVRSTVAQHHEALVGHGFTHAHIVALSQHPAALGTVAVKYQDMIAALPEATHEAIVGVGKQWSGARALEALLTVAGELRGPPLQLDTGQLLKIAKRGGVTAVEAVHAWRNALTGAPLNLTPDQVVAIASNGGGKQALETVQRLLPVLCQDHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNIGGKQALETVQRLLPVLCQAHGLTPAQVVAIANNNGGKQALETVQRLLPVLCQDHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQDHGLTPEQVVAIASNIGGKQALETVQRLLPVLCQAHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPAQVVAIANNNGGKQALETVQRLLPVLCQDHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQDHGLTPEQVVAIASHDGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPAQVVAIASNGGGKQALETVQRLLPVLCQDHGLTPDQVVAIASHDGGKQALETVQRLLPVLCQDHGLTPEQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPEQVVAIASHDGGRPALESIVAQLSRPDPALAALTNGGGGSARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQ QEQEAAELQAVTAIAEGRR 

Exemplary ATM-L-Targeting TALE Repeat Array:

(SEQ ID NO: 12) LTPDQVVAIANNNGGKQALETVQRLLPVLCQDHGLTPEQVVAIASNIGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNIGGKQALETVQRLLPVLCQAHGLTPAQVVAIASNGGGKQALETVQRLLPVLCQDHGLTPDQVVAIANGGGKQALETVQRLLPVLCQDHGLTPEQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPAQVVAIANNNGGKQALETVQRLLPVLCQDHGLTPDQVVAIASNIGGKQALETVQRLLPVLCQDHGLTPEQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPAQVVAIASHDGGKQALETVQRLLPVLCQDHGLTPDQVVAIASNGGGKQALETVQRLLPVLCQDHGLTPEQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPAQVVAIASNGGGKQALETVQRLLPVLCQDHGLTPEQVV AIASNGGGRPALE 

Exemplary ATM-Targeting TALE Construct with FLAG, NLS, and RNAPω:

(SEQ ID NO: 13) MDYKDHDGDYKDHDIDYKDDDDKMAPKKKRKVGIHRGVPMVDLRTLGYSQQQQEKIKPKVRSTVAQHHEALVGHGFTHAHIVALSQHPAALGTVAVKYQDMIAALPEATHEAIVGVGKQWSGARALEALLTVAGELRGPPLQLDTGQLLKIAKRGGVTAVEAVHAWRNALTGAPLNLTPDQVVAIANNNGGKQALETVQRLLPVLCQDHGLTPEQVVAIASNIGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNIGGKQALETVQRLLPVLCQAHGLTPAQVVAIASNGGGKQALETVQRLLPVLCQDHGLTPDQVVAIASNGGGKQALETVQRLLPVLCQDHGLTPEQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPAQVVAIANNNGGKQALETVQRLLPVLCQDHGLTPDQVVAIASNIGGKQALETVQRLLPVLCQDHGLTPEQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPDQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPAQVVAIASHDGGKQALETVQRLLPVLCQDHGLTPDQVVAIASNGGGKQALETVQRLLPVLCQDHGLTPEQVVAIANNNGGKQALETVQRLLPVLCQAHGLTPDQVVAIASNGGGKQALETVQRLLPVLCQAHGLTPAQVVAIASNGGGKQALETVQRLLPVLCQDHGLTPEQVVAIASNGGGRPALESIVAQLSRPDPALAALTNGGGGSARVTVQDVVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAELQAVTAIAE GRR 

Exemplary FokI Nuclease Domain:

(SEQ ID NO: 14) GSQLVKSELEEKKSELRHKLKYVPHEYIELIEIARNSTQDRILEMKVMEFFMKVYGYRGKHLGGSRKPDGAIYTVGSPIDYGVIVDTKAYSGGYNLPIGQADEMQRYVEENQTRNKHINPNEWWKVYPSSVTEFKFLFVSGHFKGNYKAQLTRLNHITNCNGAVLSVEELLIGGEMIKAGTLTLEEVRRKFNNGEINF

Exemplary ATM Off Target Left and Right Half-Sites, OffA1:

(SEQ ID NO: 17) TGAATaGGaAataTaTTT (SEQ ID NO: 18) TTTATTTTACTGTtTTTA

Exemplary ATM Off Target Left and Right Half-Sites, OffA11:

(SEQ ID NO: 19) TGAATTGaGAgaagcaTT (SEQ ID NO: 20) TTTATTTTAtTaTtTTTA

Exemplary ATM Off Target Left and Right Half-Sites, OffA17:

(SEQ ID NO: 21) gGAAaTGGGATaCTGagT (SEQ ID NO: 22) TTTATgTTACTaTtTcTA

Exemplary ATM Off Target Left and Right Half-Sites, OffA23:

(SEQ ID NO: 23) TagATTGaaATGCTGTTT (SEQ ID NO: 24) TTTtTaTTAtTaTtTTTA

EQUIVALENTS AND SCOPE

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents of theembodiments described herein. The scope of the present disclosure is notintended to be limited to the above description, but rather is as setforth in the appended claims.

Articles such as “a,” “an,” and “the” may mean one or more than oneunless indicated to the contrary or otherwise evident from the context.Claims or descriptions that include “or” between two or more members ofa group are considered satisfied if one, more than one, or all of thegroup members are present, unless indicated to the contrary or otherwiseevident from the context. The disclosure of a group that includes “or”between two or more group members provides embodiments in which exactlyone member of the group is present, embodiments in which more than onemembers of the group are present, and embodiments in which all of thegroup members are present. For purposes of brevity those embodimentshave not been individually spelled out herein, but it will be understoodthat each of these embodiments is provided herein and may bespecifically claimed or disclaimed.

It is to be understood that the present disclosure encompasses allvariations, combinations, and permutations in which one or morelimitation, element, clause, or descriptive term, from one or more ofthe claims or from one or more relevant portion of the description, isintroduced into another claim. For example, a claim that is dependent onanother claim can be modified to include one or more of the limitationsfound in any other claim that is dependent on the same base claim.Furthermore, where the claims recite a composition, it is to beunderstood that methods of making or using the composition according toany of the methods of making or using disclosed herein or according tomethods known in the art, if any, are included, unless otherwiseindicated or unless it would be evident to one of ordinary skill in theart that a contradiction or inconsistency would arise.

Where elements are presented as lists, e.g., in Markush group format, itis to be understood that every possible subgroup of the elements is alsodisclosed, and that any element or subgroup of elements can be removedfrom the group. It is also noted that the term “comprising” is intendedto be open and permits the inclusion of additional elements or steps. Itshould be understood that, in general, where an embodiment, product, ormethod is referred to as comprising particular elements, features, orsteps, embodiments, products, or methods that consist, or consistessentially of, such elements, features, or steps, are provided as well.For purposes of brevity those embodiments have not been individuallyspelled out herein, but it will be understood that each of theseembodiments is provided herein and may be specifically claimed ordisclaimed.

Where ranges are given, endpoints are included. Furthermore, it is to beunderstood that unless otherwise indicated or otherwise evident from thecontext and/or the understanding of one of ordinary skill in the art,values that are expressed as ranges can assume any specific value withinthe stated ranges in some embodiments, to the tenth of the unit of thelower limit of the range, unless the context clearly dictates otherwise.For purposes of brevity, the values in each range have not beenindividually spelled out herein, but it will be understood that each ofthese values is provided herein and may be specifically claimed ordisclaimed. It is also to be understood that unless otherwise indicatedor otherwise evident from the context and/or the understanding of one ofordinary skill in the art, values expressed as ranges can assume anysubrange within the given range, wherein the endpoints of the subrangeare expressed to the same degree of accuracy as the tenth of the unit ofthe lower limit of the range.

In addition, it is to be understood that any particular embodiment ofthe present disclosure may be explicitly excluded from any one or moreof the claims. Where ranges are given, any value within the range mayexplicitly be excluded from any one or more of the claims. Anyembodiment, element, feature, application, or aspect of the compositionsand/or methods of the present disclosure, can be excluded from any oneor more claims. For purposes of brevity, all of the embodiments in whichone or more elements, features, purposes, or aspects is excluded are notset forth explicitly herein.

What is claimed is:
 1. A protein comprising a transcriptionalactivator-like effector (TALE) N-terminal domain having the amino acidsequence set forth in SEQ ID NO: 1, wherein the amino acid sequencecomprises an alanine to glutamic acid amino acid substitution at aminoacid residue 39 of SEQ ID NO: 1, wherein the protein has DNA-bindingactivity.
 2. The protein of claim 1 further comprising a lysine toglutamic acid substitution at amino acid residue 19 of SEQ ID NO:
 1. 3.The protein of claim 1 further comprising a glycine to arginine aminoacid substitution at amino acid residue 98 of SEQ ID NO:
 1. 4. A proteincomprising a TALE N-terminal domain having the amino acid sequence setforth in SEQ ID NO: 1, wherein the amino acid sequence comprises alysine to glutamic acid substitution at amino acid residue 19 of SEQ IDNO: 1, wherein the protein has DNA-binding activity.
 5. The protein ofclaim 4 further comprising a glycine to arginine amino acid substitutionat amino acid residue 98 of SEQ ID NO:
 1. 6. The protein of claim 1further comprising one or more amino acid substitutions selected fromthe group consisting of S22N, G77D, A85T, T91A, A93G, P99S, P99T, A129E,and N136T of SEQ ID NO:
 1. 7. The protein of claim 1 further comprisingan arginine to tryptophan amino acid substitution at amino acid residue21 of SEQ ID NO:
 1. 8. The protein of claim 4 further comprising one ormore amino acid substitutions selected from the group consisting ofS22N, G77D, A85T, T91A, A93G, P99S, P99T, A129E, and N136T of SEQ IDNO:
 1. 9. The protein of claim 4 further comprising an arginine totryptophan amino acid substitution at amino acid residue 21 of SEQ IDNO:
 1. 10. A method comprising contacting a nucleic acid moleculecomprising a target sequence with the protein of claim 1 underconditions suitable for the protein to bind the target sequence.
 11. Themethod of claim 10, wherein the contacting is in vitro.
 12. The methodof claim 10, wherein the contacting is in vivo.
 13. The method of claim10, wherein the nucleic acid molecule is in a cell.
 14. The method ofclaim 13, wherein the cell is a mammalian cell.
 15. A method comprisingcontacting a nucleic acid molecule comprising a target sequence with theprotein of claim 4 under conditions suitable for the protein to bind thetarget sequence.
 16. The method of claim 15, wherein the contacting isin vitro.
 17. The method of claim 15, wherein the contacting is in vivo.18. The method of claim 15, wherein the nucleic acid molecule is in acell.
 19. The method of claim 18, wherein the cell is a mammalian cell.